[1] "ofn"        "-oTLUAD-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUAD-TP/22506767/LUAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUAD-TP/22815335/transformed.cor.cli.txt"

nPatients in clinical file=522, in cluster file=533, common to both=481
[1]  90 481
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           256            225 
  TP53 MUTATED TP53 WILD-TYPE 
           256            225 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
           150            331 
  KRAS MUTATED KRAS WILD-TYPE 
           150            331 
[1] "KEAP1 MUTATION ANALYSIS"
[1] 3
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             84             397 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             84             397 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
            67            414 
  EGFR MUTATED EGFR WILD-TYPE 
            67            414 
[1] "STK11 MUTATION ANALYSIS"
[1] 3
  STK11 MUTATED STK11 WILD-TYPE 
             77             404 
  STK11 MUTATED STK11 WILD-TYPE 
             77             404 
[1] "RBM10 MUTATION ANALYSIS"
[1] 3
  RBM10 MUTATED RBM10 WILD-TYPE 
             33             448 
  RBM10 MUTATED RBM10 WILD-TYPE 
             33             448 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           26           455 
  RB1 MUTATED RB1 WILD-TYPE 
           26           455 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              30              451 
  ARID1A MUTATED ARID1A WILD-TYPE 
              30              451 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           55           426 
  NF1 MUTATED NF1 WILD-TYPE 
           55           426 
[1] "SMARCA4 MUTATION ANALYSIS"
[1] 3
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               38               443 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               38               443 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
            39            442 
  BRAF MUTATED BRAF WILD-TYPE 
            39            442 
[1] "MGA MUTATION ANALYSIS"
[1] 3
  MGA MUTATED MGA WILD-TYPE 
           40           441 
  MGA MUTATED MGA WILD-TYPE 
           40           441 
[1] "FTSJD1 MUTATION ANALYSIS"
[1] 3
  FTSJD1 MUTATED FTSJD1 WILD-TYPE 
              24              457 
  FTSJD1 MUTATED FTSJD1 WILD-TYPE 
              24              457 
[1] "MET MUTATION ANALYSIS"
[1] 3
  MET MUTATED MET WILD-TYPE 
           21           460 
  MET MUTATED MET WILD-TYPE 
           21           460 
[1] "GAGE2A MUTATION ANALYSIS"
[1] 3
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               8              473 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               8              473 
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             30             451 
  SETD2 MUTATED SETD2 WILD-TYPE 
             30             451 
[1] "U2AF1 MUTATION ANALYSIS"
[1] 3
  U2AF1 MUTATED U2AF1 WILD-TYPE 
             11             470 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
             11             470 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             11             470 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             11             470 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              16              465 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              16              465 
[1] "SRPX MUTATION ANALYSIS"
[1] 3
  SRPX MUTATED SRPX WILD-TYPE 
            14            467 
  SRPX MUTATED SRPX WILD-TYPE 
            14            467 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
           42           439 
  ATM MUTATED ATM WILD-TYPE 
           42           439 
[1] "TCEAL5 MUTATION ANALYSIS"
[1] 3
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
              13              468 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
              13              468 
[1] "PPP3CA MUTATION ANALYSIS"
[1] 3
  PPP3CA MUTATED PPP3CA WILD-TYPE 
              12              469 
  PPP3CA MUTATED PPP3CA WILD-TYPE 
              12              469 
[1] "FCRLA MUTATION ANALYSIS"
[1] 3
  FCRLA MUTATED FCRLA WILD-TYPE 
             15             466 
  FCRLA MUTATED FCRLA WILD-TYPE 
             15             466 
[1] "ARID2 MUTATION ANALYSIS"
[1] 3
  ARID2 MUTATED ARID2 WILD-TYPE 
             24             457 
  ARID2 MUTATED ARID2 WILD-TYPE 
             24             457 
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
           20           461 
  APC MUTATED APC WILD-TYPE 
           20           461 
[1] "ZEB1 MUTATION ANALYSIS"
[1] 3
  ZEB1 MUTATED ZEB1 WILD-TYPE 
            32            449 
  ZEB1 MUTATED ZEB1 WILD-TYPE 
            32            449 
[1] "SIP1 MUTATION ANALYSIS"
[1] 3
  SIP1 MUTATED SIP1 WILD-TYPE 
             4            477 
  SIP1 MUTATED SIP1 WILD-TYPE 
             4            477 
[1] "SLC4A3 MUTATION ANALYSIS"
[1] 3
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
              18              463 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
              18              463 
[1] "STK19 MUTATION ANALYSIS"
[1] 3
  STK19 MUTATED STK19 WILD-TYPE 
              5             476 
  STK19 MUTATED STK19 WILD-TYPE 
              5             476 
[1] "NUDT11 MUTATION ANALYSIS"
[1] 3
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               5              476 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               5              476 
[1] "SLAMF9 MUTATION ANALYSIS"
[1] 3
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
              12              469 
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
              12              469 
[1] "DNMT3A MUTATION ANALYSIS"
[1] 3
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              19              462 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              19              462 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              19              462 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              19              462 
[1] "PTPRU MUTATION ANALYSIS"
[1] 3
  PTPRU MUTATED PTPRU WILD-TYPE 
             18             463 
  PTPRU MUTATED PTPRU WILD-TYPE 
             18             463 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              28              453 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              28              453 
[1] "ZNF608 MUTATION ANALYSIS"
[1] 3
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               9              472 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               9              472 
[1] "STIM1 MUTATION ANALYSIS"
[1] 3
  STIM1 MUTATED STIM1 WILD-TYPE 
              9             472 
  STIM1 MUTATED STIM1 WILD-TYPE 
              9             472 
[1] "EMG1 MUTATION ANALYSIS"
[1] 3
  EMG1 MUTATED EMG1 WILD-TYPE 
             5            476 
  EMG1 MUTATED EMG1 WILD-TYPE 
             5            476 
[1] "PHKA1 MUTATION ANALYSIS"
[1] 3
  PHKA1 MUTATED PHKA1 WILD-TYPE 
             12             469 
  PHKA1 MUTATED PHKA1 WILD-TYPE 
             12             469 
[1] "PAK1 MUTATION ANALYSIS"
[1] 3
  PAK1 MUTATED PAK1 WILD-TYPE 
             9            472 
  PAK1 MUTATED PAK1 WILD-TYPE 
             9            472 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             3            478 
  NRAS MUTATED NRAS WILD-TYPE 
             3            478 
[1] "G3BP1 MUTATION ANALYSIS"
[1] 3
  G3BP1 MUTATED G3BP1 WILD-TYPE 
              8             473 
  G3BP1 MUTATED G3BP1 WILD-TYPE 
              8             473 
[1] "TRERF1 MUTATION ANALYSIS"
[1] 3
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              18              463 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              18              463 
[1] "CACNA1F MUTATION ANALYSIS"
[1] 3
  CACNA1F MUTATED CACNA1F WILD-TYPE 
               27               454 
  CACNA1F MUTATED CACNA1F WILD-TYPE 
               27               454 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              13              468 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              13              468 
[1] "RPL5 MUTATION ANALYSIS"
[1] 3
  RPL5 MUTATED RPL5 WILD-TYPE 
             8            473 
  RPL5 MUTATED RPL5 WILD-TYPE 
             8            473 
[1] "STRA8 MUTATION ANALYSIS"
[1] 3
  STRA8 MUTATED STRA8 WILD-TYPE 
              8             473 
  STRA8 MUTATED STRA8 WILD-TYPE 
              8             473 
[1] "NLRP6 MUTATION ANALYSIS"
[1] 3
  NLRP6 MUTATED NLRP6 WILD-TYPE 
             10             471 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
             10             471 
[1] "FAM65C MUTATION ANALYSIS"
[1] 3
  FAM65C MUTATED FAM65C WILD-TYPE 
              14              467 
  FAM65C MUTATED FAM65C WILD-TYPE 
              14              467 
[1] "WDR66 MUTATION ANALYSIS"
[1] 3
  WDR66 MUTATED WDR66 WILD-TYPE 
             14             467 
  WDR66 MUTATED WDR66 WILD-TYPE 
             14             467 
[1] "RIT1 MUTATION ANALYSIS"
[1] 3
  RIT1 MUTATED RIT1 WILD-TYPE 
             8            473 
  RIT1 MUTATED RIT1 WILD-TYPE 
             8            473 
[1] "TGFBR3 MUTATION ANALYSIS"
[1] 3
  TGFBR3 MUTATED TGFBR3 WILD-TYPE 
              14              467 
  TGFBR3 MUTATED TGFBR3 WILD-TYPE 
              14              467 
[1] "CXCR7 MUTATION ANALYSIS"
[1] 3
  CXCR7 MUTATED CXCR7 WILD-TYPE 
             10             471 
  CXCR7 MUTATED CXCR7 WILD-TYPE 
             10             471 
[1] "GAN MUTATION ANALYSIS"
[1] 3
  GAN MUTATED GAN WILD-TYPE 
           10           471 
  GAN MUTATED GAN WILD-TYPE 
           10           471 
[1] "TMEM49 MUTATION ANALYSIS"
[1] 3
  TMEM49 MUTATED TMEM49 WILD-TYPE 
               5              476 
  TMEM49 MUTATED TMEM49 WILD-TYPE 
               5              476 
[1] "HSPA8 MUTATION ANALYSIS"
[1] 3
  HSPA8 MUTATED HSPA8 WILD-TYPE 
              9             472 
  HSPA8 MUTATED HSPA8 WILD-TYPE 
              9             472 
[1] "CD244 MUTATION ANALYSIS"
[1] 3
  CD244 MUTATED CD244 WILD-TYPE 
             12             469 
  CD244 MUTATED CD244 WILD-TYPE 
             12             469 
[1] "KIF18B MUTATION ANALYSIS"
[1] 3
  KIF18B MUTATED KIF18B WILD-TYPE 
               4              477 
  KIF18B MUTATED KIF18B WILD-TYPE 
               4              477 
[1] "PDE6A MUTATION ANALYSIS"
[1] 3
  PDE6A MUTATED PDE6A WILD-TYPE 
             16             465 
  PDE6A MUTATED PDE6A WILD-TYPE 
             16             465 
[1] "CHRND MUTATION ANALYSIS"
[1] 3
  CHRND MUTATED CHRND WILD-TYPE 
             16             465 
  CHRND MUTATED CHRND WILD-TYPE 
             16             465 
[1] "KLK1 MUTATION ANALYSIS"
[1] 3
  KLK1 MUTATED KLK1 WILD-TYPE 
             8            473 
  KLK1 MUTATED KLK1 WILD-TYPE 
             8            473 
[1] "KLHL5 MUTATION ANALYSIS"
[1] 3
  KLHL5 MUTATED KLHL5 WILD-TYPE 
             14             467 
  KLHL5 MUTATED KLHL5 WILD-TYPE 
             14             467 
[1] "DSC2 MUTATION ANALYSIS"
[1] 3
  DSC2 MUTATED DSC2 WILD-TYPE 
            20            461 
  DSC2 MUTATED DSC2 WILD-TYPE 
            20            461 
[1] "RNF160 MUTATION ANALYSIS"
[1] 3
  RNF160 MUTATED RNF160 WILD-TYPE 
              15              466 
  RNF160 MUTATED RNF160 WILD-TYPE 
              15              466 
[1] "AIFM1 MUTATION ANALYSIS"
[1] 3
  AIFM1 MUTATED AIFM1 WILD-TYPE 
             12             469 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
             12             469 
[1] "DOT1L MUTATION ANALYSIS"
[1] 3
  DOT1L MUTATED DOT1L WILD-TYPE 
             14             467 
  DOT1L MUTATED DOT1L WILD-TYPE 
             14             467 
[1] "MCM9 MUTATION ANALYSIS"
[1] 3
  MCM9 MUTATED MCM9 WILD-TYPE 
             3            478 
  MCM9 MUTATED MCM9 WILD-TYPE 
             3            478 
[1] "NCKAP1L MUTATION ANALYSIS"
[1] 3
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
               19               462 
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
               19               462 
[1] "ESYT3 MUTATION ANALYSIS"
[1] 3
  ESYT3 MUTATED ESYT3 WILD-TYPE 
              8             473 
  ESYT3 MUTATED ESYT3 WILD-TYPE 
              8             473 
[1] "MIA2 MUTATION ANALYSIS"
[1] 3
  MIA2 MUTATED MIA2 WILD-TYPE 
            13            468 
  MIA2 MUTATED MIA2 WILD-TYPE 
            13            468 
[1] "TUBB4 MUTATION ANALYSIS"
[1] 3
  TUBB4 MUTATED TUBB4 WILD-TYPE 
             17             464 
  TUBB4 MUTATED TUBB4 WILD-TYPE 
             17             464 
[1] "ABHD12B MUTATION ANALYSIS"
[1] 3
  ABHD12B MUTATED ABHD12B WILD-TYPE 
                7               474 
  ABHD12B MUTATED ABHD12B WILD-TYPE 
                7               474 
[1] "ANTXR1 MUTATION ANALYSIS"
[1] 3
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
              19              462 
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
              19              462 
[1] "FLCN MUTATION ANALYSIS"
[1] 3
  FLCN MUTATED FLCN WILD-TYPE 
             9            472 
  FLCN MUTATED FLCN WILD-TYPE 
             9            472 
[1] "ZNF556 MUTATION ANALYSIS"
[1] 3
  ZNF556 MUTATED ZNF556 WILD-TYPE 
              12              469 
  ZNF556 MUTATED ZNF556 WILD-TYPE 
              12              469 
[1] "ASCL3 MUTATION ANALYSIS"
[1] 3
  ASCL3 MUTATED ASCL3 WILD-TYPE 
              7             474 
  ASCL3 MUTATED ASCL3 WILD-TYPE 
              7             474 
[1] "DSG3 MUTATION ANALYSIS"
[1] 3
  DSG3 MUTATED DSG3 WILD-TYPE 
            33            448 
  DSG3 MUTATED DSG3 WILD-TYPE 
            33            448 
[1] "C5AR1 MUTATION ANALYSIS"
[1] 3
  C5AR1 MUTATED C5AR1 WILD-TYPE 
              6             475 
  C5AR1 MUTATED C5AR1 WILD-TYPE 
              6             475 
[1] "ASXL2 MUTATION ANALYSIS"
[1] 3
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             18             463 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             18             463 
[1] "DLX5 MUTATION ANALYSIS"
[1] 3
  DLX5 MUTATED DLX5 WILD-TYPE 
            13            468 
  DLX5 MUTATED DLX5 WILD-TYPE 
            13            468 
[1] "ATAD2 MUTATION ANALYSIS"
[1] 3
  ATAD2 MUTATED ATAD2 WILD-TYPE 
             14             467 
  ATAD2 MUTATED ATAD2 WILD-TYPE 
             14             467 
[1] "RAF1 MUTATION ANALYSIS"
[1] 3
  RAF1 MUTATED RAF1 WILD-TYPE 
             6            475 
  RAF1 MUTATED RAF1 WILD-TYPE 
             6            475 
[1] "A2M MUTATION ANALYSIS"
[1] 3
  A2M MUTATED A2M WILD-TYPE 
           20           461 
  A2M MUTATED A2M WILD-TYPE 
           20           461 
[1] "SND1 MUTATION ANALYSIS"
[1] 3
  SND1 MUTATED SND1 WILD-TYPE 
            16            465 
  SND1 MUTATED SND1 WILD-TYPE 
            16            465 
[1] "C7ORF36 MUTATION ANALYSIS"
[1] 3
  C7ORF36 MUTATED C7ORF36 WILD-TYPE 
                6               475 
  C7ORF36 MUTATED C7ORF36 WILD-TYPE 
                6               475 
[1] "HTRA1 MUTATION ANALYSIS"
[1] 3
  HTRA1 MUTATED HTRA1 WILD-TYPE 
             10             471 
  HTRA1 MUTATED HTRA1 WILD-TYPE 
             10             471 
[1] "ADAMTS2 MUTATION ANALYSIS"
[1] 3
  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
               39               442 
  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
               39               442 
[1] "TAF1L MUTATION ANALYSIS"
[1] 3
  TAF1L MUTATED TAF1L WILD-TYPE 
             50             431 
  TAF1L MUTATED TAF1L WILD-TYPE 
             50             431 
[1] "PLEKHB2 MUTATION ANALYSIS"
[1] 3
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                6               475 
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                6               475 
[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 481 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=163,	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=268,	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=4,	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=90,	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 481 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 
156 261  43  18 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
156 261  43  18 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
156 261  43  18 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
156 261  43  18 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
308  89  70   2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
  308    89    72 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
308  89  70   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
  308    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=90, 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   156  96
  TP53 WILD-TYPE 142  75
  TP53 MUTATED TP53 WILD-TYPE 
           252            217 
  TP53 MUTATED TP53 WILD-TYPE 
            96             75 
$`TP53 MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4427 
       19.96        14.01         9.96         8.02        20.05        26.01 
TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-44-6147 TCGA-44-7661 TCGA-44-7670 
       28.41        35.28        14.73        27.78        18.31        29.00 
TCGA-55-1592 TCGA-55-6979 TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 TCGA-55-7914 
       23.05         7.79        16.01        23.18        21.44         6.15 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       16.93        19.69        18.15        13.68        16.93        22.65 
TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 TCGA-78-8660 TCGA-91-6836 TCGA-91-A4BC 
       20.58        20.19        20.65        10.55        13.71         1.45 
TCGA-93-8067 TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-97-8172 TCGA-97-A4LX 
        6.12        16.54         2.86        15.68        17.92        20.19 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4395 TCGA-05-4397 
       10.09        27.19        31.23         2.43         0.00        24.03 
TCGA-05-4398 TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 TCGA-05-4426 TCGA-05-4430 
       47.05         2.99        29.98        30.02        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 
       25.02        24.00         4.96        29.00        22.03         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4632 TCGA-44-2656 TCGA-44-3396 
        5.98         8.68        97.74        44.61        46.98        37.15 
TCGA-44-3918 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       34.06        33.30        28.37        28.01        23.77        19.56 
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-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
        7.17        36.07        18.87        12.66         8.55        15.98 
TCGA-44-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-49-4505 TCGA-49-4514 TCGA-49-6767 TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 
       14.07        55.89        22.26        71.47       101.72        47.41 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 
       49.28         9.27        14.27        78.67        15.12        48.46 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       57.53        53.16        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       12.16         6.21         0.72        27.25        34.29        30.54 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6975 
       35.21        30.58         5.62        42.51        40.73         3.88 
TCGA-55-6985 TCGA-55-7227 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       40.54        31.30        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 
        3.91        18.64        11.28        34.19        17.65        18.44 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       19.82        29.23        29.72        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 
       23.64        22.16        15.42        17.56        15.72         0.36 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 
       13.74        17.72        17.10        17.62         1.58        12.33 
TCGA-55-A48Z TCGA-55-A493 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8399 TCGA-62-8402 
       21.40         0.92        19.99         4.57        88.64        49.25 
TCGA-62-A46O TCGA-62-A46R TCGA-62-A46U TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 
       47.80        56.71        67.96        13.61        40.96        29.92 
TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-67-3771 
       56.81        81.80        38.37         2.04        42.90        20.05 
TCGA-69-7760 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        6.64         5.42         6.05         4.41        13.41        13.51 
TCGA-69-8255 TCGA-69-A59K TCGA-71-8520 TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 
        4.24        19.43         6.90        26.30         4.31         9.24 
TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6214 TCGA-78-7143 
       50.33        66.64        77.85        43.82        36.66       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7154 
       27.16         5.69        19.27       129.53        21.90        19.50 
TCGA-78-7155 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 
       38.50        26.53        31.20         8.02        39.35        10.55 
TCGA-78-8640 TCGA-78-8662 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      232.18       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        11.61         0.62 
TCGA-86-8673 TCGA-86-A4JF TCGA-86-A4P7 TCGA-91-6829 TCGA-91-6831 TCGA-91-6840 
       28.34        24.23        13.64        41.36        10.19        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       27.68         7.36         1.18        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-97-7553 
       41.82        18.67        12.39        27.29         2.76        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 
       25.48        18.54         0.59        18.12        14.30        21.60 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 
       21.44        19.76        24.56        34.85        36.76        21.57 
TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T4 
       18.08        19.00        38.63         2.76        86.14        86.04 
TCGA-MP-A4T9 TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-O1-A52J 
       41.59        11.05        14.10        19.13        71.05        59.11 

$`TP53 WILD-TYPE`
TCGA-05-4418 TCGA-05-4434 TCGA-05-5420 TCGA-38-4631 TCGA-38-7271 TCGA-44-2661 
        9.01        15.02        15.02        11.64        26.30        38.10 
TCGA-44-6146 TCGA-44-6776 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       23.93        86.01        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 TCGA-55-7725 TCGA-55-8090 TCGA-55-8091 
       48.62         5.79         7.99        14.53        19.66        19.73 
TCGA-55-8203 TCGA-55-8207 TCGA-55-A492 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       17.98        32.12        19.59        13.87        52.60        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-80-5611 TCGA-91-7771 TCGA-93-A4JQ 
       39.09         8.48        50.24        85.32        16.18        17.29 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       15.65        21.40        18.18        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-MP-A4T8 TCGA-MP-A4TD TCGA-05-4249 
       24.30        23.80         6.35         5.29        10.09        50.07 
TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4403 TCGA-05-4417 TCGA-05-4422 
        3.98        45.01        37.02        19.00        14.96        12.00 
TCGA-05-4425 TCGA-05-5429 TCGA-05-5715 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
       21.99         9.04         2.04       120.79        37.71        49.05 
TCGA-38-A44F TCGA-44-2657 TCGA-44-2665 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
        4.37        44.42        42.77        38.24        33.73        26.56 
TCGA-44-6148 TCGA-44-7659 TCGA-44-7672 TCGA-44-A47A TCGA-44-A47B TCGA-49-4486 
       23.15        22.72        23.64        15.32         9.44        76.21 
TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 
       35.54        32.84         8.81        29.46        29.75        53.29 
TCGA-49-6744 TCGA-50-5044 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5936 
       55.33        20.52        15.72        60.16         8.22         8.45 
TCGA-50-5942 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-53-7813 TCGA-55-6543 
       60.72        10.13        36.99        36.79        13.94        14.30 
TCGA-55-6642 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6981 
       80.52        15.25        46.03        53.65        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       32.71        92.81        24.99       107.21        70.26        28.67 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-8087 TCGA-55-8097 TCGA-55-8206 
       23.15        25.41        15.39        15.19        15.65        29.19 
TCGA-55-8505 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-A48Y 
       14.47        20.28        19.96        26.01        14.66        20.71 
TCGA-55-A490 TCGA-55-A494 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-A46P 
        3.25        15.81        39.98        42.38        14.60        19.53 
TCGA-62-A46S TCGA-62-A46V TCGA-62-A470 TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 
       54.35        72.30        39.25        87.98        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-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-8253 TCGA-69-8254 
        6.12        22.68        13.61         7.56        14.01        13.45 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4668 TCGA-73-4675 TCGA-73-4677 TCGA-75-6206 
        8.42        23.38        15.35        30.31         1.25        85.15 
TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 TCGA-78-7148 TCGA-78-7152 TCGA-78-7153 
       49.84       108.66       100.57        20.58        39.95       119.51 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7537 TCGA-78-7539 TCGA-78-8648 TCGA-78-8655 
      238.29        88.14        53.33        26.01        39.75        77.59 
TCGA-80-5608 TCGA-86-6562 TCGA-86-7713 TCGA-86-7714 TCGA-86-7955 TCGA-86-8054 
       93.11        12.36        38.04        20.55        35.24        37.74 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       32.65        31.04        14.60        13.91        30.84        27.58 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 
       26.50        29.46        26.47        10.62         1.97         2.60 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
        1.15        16.60        14.27        19.82        22.45        17.46 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7941 TCGA-97-8171 
       19.89        42.25        64.60        63.52        15.91        18.67 
TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M5 TCGA-97-A4M6 
        5.39        15.39        16.41        20.58        20.84        18.67 
TCGA-99-8032 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-MP-A4SW TCGA-MP-A4SY 
        1.45        35.47        32.48        14.30        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A5C7 
       37.35        58.85         5.49        29.46        24.36        73.91 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       74.33         0.13         1.64        47.08         0.49         0.43 
TCGA-NJ-A55R 
       19.82 

  TP53 MUTATED TP53 WILD-TYPE 
          0.00           0.13 
  TP53 MUTATED TP53 WILD-TYPE 
        232.18         238.29 
  TP53 MUTATED TP53 WILD-TYPE 
        20.615         22.720 
[1] "0.0 - 232.2 (20.6)" "0.1 - 238.3 (22.7)"
[1] "hr=" "1.4"
D1V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TP53 MUTATED         3       60       73        25        34         36
  TP53 WILD-TYPE       1       61       59        21        32         34
                vv
clus             STAGE IIIB STAGE IV
  TP53 MUTATED            8       14
  TP53 WILD-TYPE          3       10
D1V3, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE I               3              1
  STAGE IA             60             61
  STAGE IB             73             59
  STAGE IIA            25             21
  STAGE IIB            34             32
  STAGE IIIA           36             34
  STAGE IIIB            8              3
  STAGE IV             14             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    80 142  20  12
  TP53 WILD-TYPE  76 119  23   6
D1V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1           80             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   165  47    38
  TP53 WILD-TYPE 143  42    34
D1V5, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  N0             165            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   139 117
  TP53 WILD-TYPE 121 104
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    139  117
  TP53 WILD-TYPE  121  104
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE          139            121
  MALE            117            104
[1] 2 2
[1] FALSE
D1V8, binary
                cls
clus               0   1
  TP53 MUTATED   195  37
  TP53 WILD-TYPE 189  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    195   37
  TP53 WILD-TYPE  189   18
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO           195            189
  YES           37             18
[1] 2 2
[1] FALSE
D1V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TP53 MUTATED                            7                                52
  TP53 WILD-TYPE                         10                                50
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TP53 MUTATED                                                  173
  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                                    7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            52
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          173
  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   165   6   1  14
  TP53 WILD-TYPE 147   6   3  11
D1V13, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0          165            147
  R1            6              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                          23   197
  TP53 WILD-TYPE                         7   181
D1V14, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              4
  BLACK OR AFRICAN AMERICAN                  23              7
  WHITE                                     197            181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V15, binary
                cls
clus               0   1
  TP53 MUTATED     6 189
  TP53 WILD-TYPE   0 162
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      6  189
  TP53 WILD-TYPE    0  162
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                6              0
  NOT HISPANIC OR LATINO          189            162
[1] 2 2
[1] FALSE

Clustering(2) Variable = KRAS MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  KRAS MUTATED    95  52
  KRAS WILD-TYPE 203 119
  KRAS MUTATED KRAS WILD-TYPE 
           147            322 
  KRAS MUTATED KRAS WILD-TYPE 
            52            119 
$`KRAS MUTATED`
TCGA-05-4418 TCGA-05-4427 TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 
        9.01        26.01        23.93        86.01        18.31        29.23 
TCGA-44-A47F TCGA-49-6761 TCGA-50-5932 TCGA-55-1595 TCGA-55-7284 TCGA-55-7725 
       11.08        11.64        40.60        48.62         7.99        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 TCGA-55-8207 TCGA-73-4662 
       21.44         6.15        19.66        17.98        32.12        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-91-6836 TCGA-93-8067 TCGA-95-7562 TCGA-95-A4VK 
       39.09         8.48        13.71         6.12         2.86        21.40 
TCGA-95-A4VN TCGA-J2-8194 TCGA-L9-A443 TCGA-MP-A4T8 TCGA-MP-A4TD TCGA-05-4249 
       18.18        23.80         6.35         5.29        10.09        50.07 
TCGA-05-4250 TCGA-05-4390 TCGA-05-4395 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        3.98        37.02         0.00        19.00         2.99        14.96 
TCGA-05-4433 TCGA-38-4626 TCGA-44-6145 TCGA-44-6777 TCGA-44-7659 TCGA-44-7672 
       24.00       120.79        19.56        32.45        22.72        23.64 
TCGA-44-8117 TCGA-44-A47A TCGA-49-4505 TCGA-49-4510 TCGA-50-5051 TCGA-50-5941 
       12.66        15.32        14.07        29.46        15.72        48.46 
TCGA-50-8457 TCGA-50-8459 TCGA-53-7813 TCGA-55-6642 TCGA-55-6970 TCGA-55-6975 
       36.99        36.79        13.94        80.52        15.25         3.88 
TCGA-55-6983 TCGA-55-6984 TCGA-55-7281 TCGA-55-7283 TCGA-55-7576 TCGA-55-7728 
       92.81        24.99        28.67        20.02        22.03        23.15 
TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-8094 TCGA-55-8097 
       25.41        11.28        34.19        17.65        17.79        15.65 
TCGA-55-8299 TCGA-55-8302 TCGA-55-8508 TCGA-55-8512 TCGA-55-8514 TCGA-55-8615 
       15.42        15.72        20.28        19.96        17.10        14.66 
TCGA-55-8616 TCGA-55-A490 TCGA-55-A494 TCGA-62-8398 TCGA-62-A46R TCGA-62-A46S 
        1.58         3.25        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        13.51        14.01        13.45 
TCGA-73-4659 TCGA-73-4670 TCGA-73-4677 TCGA-75-6206 TCGA-75-7027 TCGA-78-7145 
       23.38         4.31         1.25        85.15       100.57        27.16 
TCGA-78-7148 TCGA-78-7160 TCGA-78-7161 TCGA-78-7167 TCGA-78-7539 TCGA-78-7540 
       20.58        22.92         9.57        88.14        26.01        39.35 
TCGA-78-8655 TCGA-80-5608 TCGA-83-5908 TCGA-86-7713 TCGA-86-7953 TCGA-86-8054 
       77.59        93.11        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-91-8497 TCGA-93-7347 TCGA-93-A4JO TCGA-95-7039 TCGA-95-7567 
       10.62        14.27        22.45         1.08        41.82        18.67 
TCGA-95-A4VP TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8176 TCGA-97-8179 
       19.89        25.48         0.59        15.91        15.39        14.30 
TCGA-97-A4M0 TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       21.44        20.84        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-A4AG TCGA-MN-A4N5 TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T7 
       21.57        32.48         2.76        49.35        86.04         5.49 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YG TCGA-NJ-A4YI 
       29.46        11.05        14.10        19.13        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A55O TCGA-NJ-A55R 
        1.64         0.43        19.82 

$`KRAS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4434 
       19.96        14.01         9.96         8.02        20.05        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       15.02        28.41        35.28        11.64        14.73        26.30 
TCGA-44-2661 TCGA-44-6147 TCGA-44-7670 TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 
       38.10        27.78        29.00         9.37        46.72        16.04 
TCGA-49-6745 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-6978 TCGA-55-6979 
       17.16        21.47        41.69        23.05         5.79         7.79 
TCGA-55-7573 TCGA-55-7724 TCGA-55-8091 TCGA-55-8204 TCGA-55-8205 TCGA-55-8511 
       16.01        23.18        19.73        16.93        19.69        18.15 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF 
       13.68        16.93        22.65        20.58        19.59        20.19 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       20.65        13.87        52.60        50.24        10.55        85.32 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 
       16.18         1.45        17.29        16.54        15.68        15.65 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4389 TCGA-05-4397 
       10.09        27.19        31.23         2.43        45.01        24.03 
TCGA-05-4398 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       47.05        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       25.02        25.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 
        2.04         7.40         5.98         8.68        97.74        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         4.37        46.98        44.42        42.77 
TCGA-44-3396 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-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.37        28.01        23.77        23.15        21.63        23.18 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       61.28        16.44        19.46         7.17        36.07        18.87 
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-49-4506 
       76.21        28.11        28.57        12.66        35.54        32.84 
TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 
        8.81        29.75        55.89        53.29        55.33        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       20.52        71.47       101.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
        8.22         9.27        14.27        78.67         8.45        15.12 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       60.72        57.53        53.16        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8460 
       11.05        12.16         6.21         0.72        10.13        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 
       34.29        30.54        35.21        30.58        14.30         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6981 
       42.51        40.73        46.03        53.65        69.34        45.34 
TCGA-55-6982 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7570 
       32.71        40.54       107.21        70.26        31.30        27.09 
TCGA-55-7574 TCGA-55-7727 TCGA-55-7816 TCGA-55-7903 TCGA-55-7913 TCGA-55-7994 
       32.71         3.91        15.39        18.64        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8096 
       29.23        29.72        15.19        23.08         5.06        23.64 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       29.19        22.16        17.56        14.47         0.36        13.74 
TCGA-55-8510 TCGA-55-8513 TCGA-55-8614 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.72        26.01        17.62        12.33        20.71        21.40 
TCGA-55-A493 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
        0.92        19.99         4.57        39.98        42.38        88.64 
TCGA-62-8402 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-64-1679 TCGA-64-1681 
       39.25        40.96        29.92        56.81        81.80        38.37 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 TCGA-67-6216 
       28.41        51.25        20.05        18.84         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 
        6.64         6.12        22.68        13.61         5.42        13.41 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4666 TCGA-73-4668 
        4.24        19.43         8.42         6.90        26.30        15.35 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
       30.31         9.24        50.33        66.64        77.85        43.82 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 
       49.84        36.66       108.66       163.10         5.69        19.27 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
      129.53        21.90        39.95       119.51        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 TCGA-78-7220 
       32.09         5.88        64.90       104.19       238.29        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
       31.20         8.02        53.33        10.55       232.18        39.75 
TCGA-78-8662 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 
      110.50        12.36         5.88        31.13        34.39        20.55 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       19.89        35.24         4.08        24.33         0.79        22.82 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 
       31.04        31.20        23.05        21.47        11.61        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-A4P7 TCGA-86-A4P8 
       30.84        27.58         0.62        28.34        13.64        26.47 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
       41.36         1.97        10.19         2.60        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7348 
        7.36         1.15        16.60         1.18        19.82        17.46 
TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 
       23.61        19.00        12.39        27.29         2.76        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-8171 TCGA-97-8174 
       64.60        63.52        61.48        18.54        18.67         5.39 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M6 
       18.12        16.41        21.60        20.58        19.76        18.67 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MP-A4SV 
       18.08        35.47        19.00        14.30        38.63        86.14 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A5C7 
       58.45        37.35        58.85        41.59        24.36        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-O1-A52J 
       71.05        47.08         0.49        59.11 

  KRAS MUTATED KRAS WILD-TYPE 
          0.00           0.36 
  KRAS MUTATED KRAS WILD-TYPE 
        120.79         238.29 
  KRAS MUTATED KRAS WILD-TYPE 
        19.820         22.665 
[1] "0.0 - 120.8 (19.8)" "0.4 - 238.3 (22.7)"
[1] "hr=" "1.2"
D2V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KRAS MUTATED         1       36       33        15        25         24
  KRAS WILD-TYPE       3       85       99        31        41         46
                vv
clus             STAGE IIIB STAGE IV
  KRAS MUTATED            3        9
  KRAS WILD-TYPE          8       15
D2V3, multiclass
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  STAGE I               1              3
  STAGE IA             36             85
  STAGE IB             33             99
  STAGE IIA            15             31
  STAGE IIB            25             41
  STAGE IIIA           24             46
  STAGE IIIB            3              8
  STAGE IV              9             15
[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 114 179  26  10
D2V4, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  T1           42            114
  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 214  59    49
D2V5, multiclass
       clus
vv      KRAS MUTATED KRAS WILD-TYPE
  N0              94            214
  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 179 152
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     81   69
  KRAS WILD-TYPE  179  152
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE           81            179
  MALE             69            152
[1] 2 2
[1] FALSE
D2V8, binary
                cls
clus               0   1
  KRAS MUTATED   127  11
  KRAS WILD-TYPE 257  44
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED    127   11
  KRAS WILD-TYPE  257   44
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO           127            257
  YES           11             44
[1] 2 2
[1] FALSE
D2V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KRAS MUTATED                            6                                32
  KRAS WILD-TYPE                         11                                70
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KRAS MUTATED                                                   85
  KRAS WILD-TYPE                                                211
                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                                     11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              70
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            211
  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 214   9   2  17
D2V13, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0           98            214
  R1            3              9
  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   115
  KRAS WILD-TYPE                        19   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             19
  WHITE                                     115            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     0 109
  KRAS WILD-TYPE   6 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0  109
  KRAS WILD-TYPE    6  242
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO          109            242
[1] 2 2
[1] FALSE

Clustering(3) Variable = KEAP1 MUTATION ANALYSIS
D3V1, survival
                 sevent
clus2               0   1
  KEAP1 MUTATED    45  37
  KEAP1 WILD-TYPE 253 134
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             82             387 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
             37             134 
$`KEAP1 MUTATED`
TCGA-05-4384 TCGA-05-4418 TCGA-38-4631 TCGA-44-6776 TCGA-44-7671 TCGA-44-A47F 
       14.01         9.01        11.64        86.01        29.23        11.08 
TCGA-49-6742 TCGA-55-A492 TCGA-55-A4DF TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       16.04        19.59        20.19        39.09         8.48        50.24 
TCGA-95-7043 TCGA-95-7947 TCGA-97-A4M3 TCGA-J2-8194 TCGA-05-4389 TCGA-05-4395 
       16.54        15.68        17.75        23.80        45.01         0.00 
TCGA-35-5375 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 
        8.68        61.28        16.44        19.46        36.07        18.87 
TCGA-44-A4SS TCGA-49-4486 TCGA-49-4488 TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 
       13.64        76.21        28.57        32.84         8.81        55.89 
TCGA-49-6743 TCGA-50-5051 TCGA-50-5068 TCGA-50-5936 TCGA-50-5939 TCGA-53-7624 
       53.29        15.72        49.28         8.45        15.12        34.29 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6970 TCGA-55-6972 TCGA-55-6987 TCGA-55-7815 
       35.21        30.58        15.25        53.65        70.26        25.41 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8094 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       29.23        29.72        17.79        15.72        14.47         0.36 
TCGA-55-8510 TCGA-55-8620 TCGA-62-8398 TCGA-62-A46O TCGA-62-A470 TCGA-64-5781 
       17.72        12.33        14.60        47.80        39.25        51.25 
TCGA-67-3771 TCGA-69-8253 TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 
       20.05        14.01        26.30         4.31         9.24         1.25 
TCGA-75-6206 TCGA-75-7027 TCGA-78-7146 TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 
       85.15       100.57         5.69       129.53       119.51        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 TCGA-78-7167 TCGA-86-8358 TCGA-86-8674 
       32.09         5.88       104.19        88.14        21.47        26.50 
TCGA-91-6848 TCGA-91-6849 TCGA-97-8176 TCGA-97-8179 TCGA-99-8033 TCGA-MP-A4T7 
        7.36         1.15        15.39        14.30        21.57         5.49 
TCGA-MP-A4TE TCGA-MP-A5C7 TCGA-NJ-A4YQ TCGA-NJ-A55R 
       29.46        73.91        47.08        19.82 

$`KEAP1 WILD-TYPE`
TCGA-05-4382 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4427 TCGA-05-4434 
       19.96         9.96         8.02        20.05        26.01        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 
       15.02        28.41        35.28        14.73        26.30        38.10 
TCGA-44-6146 TCGA-44-6147 TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 TCGA-49-4501 
       23.93        27.78        18.31        29.00         9.37        46.72 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       22.65        20.58        20.65        13.87        52.60        82.68 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
       17.29         2.86        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M7 TCGA-J2-8192 TCGA-L9-A443 TCGA-L9-A444 
       20.19        20.52        20.68        24.30         6.35        10.09 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 
       27.19         5.29        31.23         2.43        10.09        50.07 
TCGA-05-4250 TCGA-05-4390 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
        3.98        37.02        24.03        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        24.00         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 
        9.04         2.04         7.40         5.98        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       37.71        49.05        44.61         4.37        46.98        44.42 
TCGA-44-2665 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-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 TCGA-44-7662 TCGA-44-7672 
       21.63        23.18        32.45        22.72         7.17        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       12.66         8.55        15.98        15.32         9.44        11.54 
TCGA-44-A4SU TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4510 
       13.45        28.11        12.66        35.54        14.07        29.46 
TCGA-49-4512 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       29.75        55.33        22.26        20.52        71.47       101.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       60.16        47.41         8.22         9.27        14.27        78.67 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       48.46        60.72        57.53        53.16        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05        12.16         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-55-6543 
       36.99        36.79        27.25        30.54        13.94        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6975 
       80.52         5.62        42.51        40.73        46.03         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
      107.21        31.30        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
       22.03         3.91        23.15        15.39        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-8087 TCGA-55-8089 
       34.19        17.65        18.44        19.82        15.19        23.08 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
        5.06        23.64        15.65        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       17.56        13.74        20.28        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       17.62        14.66         1.58        20.71        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        19.99         4.57        39.98        42.38 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       88.64        49.25        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 
       72.30        13.61        40.96        29.92        56.81        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 
       38.37        87.98         2.04        42.90        28.41        28.47 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       18.84        14.04        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        4.41        13.41        13.51        13.45         4.24        19.43 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4668 TCGA-73-4675 TCGA-73-7499 
        8.42         6.90        23.38        15.35        30.31        50.33 
TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       66.64        77.85        43.82        49.84        36.66       108.66 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 
      163.10        27.16        19.27        20.58        21.90        39.95 
TCGA-78-7155 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7220 
       38.50        64.90        22.92         9.57       238.29        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 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        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
        0.62        28.34        29.46        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
       10.62        41.36         1.97        10.19         2.60        12.23 
TCGA-91-6847 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
       27.68        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 
       17.46        23.61         1.08        19.00        41.82        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       12.39        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 
       18.67         5.39        18.12        16.41        21.60        20.58 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       36.76         1.45        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       14.30        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TF TCGA-MP-A4TH 
       37.35        86.04        58.85        41.59        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       14.10        19.13        71.05        74.33         0.13         1.64 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J 
        0.49         0.43        59.11 

  KEAP1 MUTATED KEAP1 WILD-TYPE 
           0.00            0.13 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
         129.53          238.29 
  KEAP1 MUTATED KEAP1 WILD-TYPE 
         19.935          21.630 
[1] "0.0 - 129.5 (19.9)" "0.1 - 238.3 (21.6)"
[1] "hr=" "1.2"
D3V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  KEAP1 MUTATED         0       22       18         7         8         15
  KEAP1 WILD-TYPE       4       99      114        39        58         55
                 vv
clus              STAGE IIIB STAGE IV
  KEAP1 MUTATED            3        9
  KEAP1 WILD-TYPE          8       15
D3V3, multiclass
            clus
vv           KEAP1 MUTATED KEAP1 WILD-TYPE
  STAGE I                0               4
  STAGE IA              22              99
  STAGE IB              18             114
  STAGE IIA              7              39
  STAGE IIB              8              58
  STAGE IIIA            15              55
  STAGE IIIB             3               8
  STAGE IV               9              15
[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 127 218  36  14
D3V4, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  T1            29             127
  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 257  73    57
D3V5, multiclass
       clus
vv      KEAP1 MUTATED KEAP1 WILD-TYPE
  N0               51             257
  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 224 173
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED     36   48
  KEAP1 WILD-TYPE  224  173
        clus
vv       KEAP1 MUTATED KEAP1 WILD-TYPE
  FEMALE            36             224
  MALE              48             173
[1] 2 2
[1] FALSE
D3V8, binary
                 cls
clus                0   1
  KEAP1 MUTATED    61  14
  KEAP1 WILD-TYPE 323  41
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED     61   14
  KEAP1 WILD-TYPE  323   41
     clus
vv    KEAP1 MUTATED KEAP1 WILD-TYPE
  NO             61             323
  YES            14              41
[1] 2 2
[1] FALSE
D3V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KEAP1 MUTATED                            4                                20
  KEAP1 WILD-TYPE                         13                                82
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KEAP1 MUTATED                                                   50
  KEAP1 WILD-TYPE                                                246
                 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                                      13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               82
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             246
  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 258   9   4  21
D3V13, multiclass
    clus
vv   KEAP1 MUTATED KEAP1 WILD-TYPE
  R0            54             258
  R1             3               9
  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                        24   309
D3V14, multiclass
                                  clus
vv                                 KEAP1 MUTATED KEAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    6              24
  WHITE                                       69             309
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V15, binary
                 cls
clus                0   1
  KEAP1 MUTATED     2  56
  KEAP1 WILD-TYPE   4 295
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KEAP1 MUTATED      2   56
  KEAP1 WILD-TYPE    4  295
                        clus
vv                       KEAP1 MUTATED KEAP1 WILD-TYPE
  HISPANIC OR LATINO                 2               4
  NOT HISPANIC OR LATINO            56             295
[1] 2 2
[1] FALSE

Clustering(4) Variable = EGFR MUTATION ANALYSIS
D4V1, survival
                sevent
clus2              0   1
  EGFR MUTATED    37  28
  EGFR WILD-TYPE 261 143
  EGFR MUTATED EGFR WILD-TYPE 
            65            404 
  EGFR MUTATED EGFR WILD-TYPE 
            28            143 
$`EGFR MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-38-4629 TCGA-38-6178 TCGA-44-2661 TCGA-44-6147 
       19.96         8.02        28.41        14.73        38.10        27.78 
TCGA-49-4501 TCGA-55-7573 TCGA-67-6217 TCGA-95-7947 TCGA-97-8172 TCGA-97-A4M7 
       46.72        16.01        13.87        15.68        17.92        20.68 
TCGA-J2-8192 TCGA-05-5423 TCGA-05-5425 TCGA-38-4627 TCGA-38-4628 TCGA-44-A4SU 
       24.30         4.96        29.00        37.71        49.05        13.45 
TCGA-49-4490 TCGA-49-4494 TCGA-50-5066 TCGA-50-5944 TCGA-50-6591 TCGA-50-6595 
       12.66        35.54        47.41        57.53         3.91         6.21 
TCGA-50-6673 TCGA-55-6968 TCGA-55-6980 TCGA-55-6981 TCGA-55-7570 TCGA-55-8096 
        0.72        42.51        69.34        45.34        27.09        23.64 
TCGA-55-8206 TCGA-55-8506 TCGA-55-A48Z TCGA-62-8394 TCGA-62-8402 TCGA-62-A46U 
       29.19         0.36        21.40         4.57        49.25        67.96 
TCGA-64-1681 TCGA-67-3772 TCGA-69-7760 TCGA-69-7765 TCGA-71-8520 TCGA-75-6212 
       38.37        18.84         6.64         5.42         6.90        49.84 
TCGA-75-7025 TCGA-78-7147 TCGA-78-7155 TCGA-78-7158 TCGA-86-8055 TCGA-86-8074 
      108.66        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-97-8171 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 
       19.00        41.82        18.67        16.41        21.60        20.58 
TCGA-97-A4M1 TCGA-97-A4M6 TCGA-MP-A4SW TCGA-MP-A4T6 TCGA-MP-A4T9 
       19.76        18.67        58.45        58.85        41.59 

$`EGFR WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 
       14.01         9.96        20.05         9.01        26.01        15.02 
TCGA-05-5420 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-44-6146 TCGA-44-6776 
       15.02        35.28        11.64        26.30        23.93        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-6742 
       18.31        29.00        29.23         9.37        11.08        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7724 TCGA-55-7725 
       48.62         5.79         7.79         7.99        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       21.44         6.15        19.66        19.73        17.98        16.93 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       19.69        32.12        18.15        13.68        16.93        22.65 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 
       20.58        19.59        20.19        20.65        52.60        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 
       39.09         8.48        50.24        10.55        85.32        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       16.18         1.45         6.12        17.29        16.54         2.86 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       15.65        21.40        18.18        20.19        20.52        17.75 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       29.98        12.00        30.02        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
       25.02        24.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4632 TCGA-38-A44F 
        5.98         8.68        97.74       120.79        44.61         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       46.98        44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       19.56        23.15        21.63        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        22.72        19.46         7.17        36.07        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         8.55        15.98        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4505 
       11.54        13.64        76.21        28.11        28.57        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       55.33        22.26        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       60.16        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 
        8.45        15.12        48.46        60.72        53.16        42.35 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       25.55        11.05        12.16        10.13        36.99        36.79 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 
       27.25        34.29        30.54        13.94        35.21        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       14.30        80.52         5.62        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       53.65         3.88        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7574 
      107.21        70.26        31.30        28.67        20.02        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
       22.03         3.91        23.15        25.41        15.39        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 
       11.28        34.19        17.65        18.44        19.82        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 
       29.72        15.19        23.08         5.06        17.79        15.65 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
       22.16        15.42        17.56        15.72        14.47        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A493 
       14.66         1.58        12.33        20.71         3.25         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       15.81        19.99        39.98        42.38        14.60        88.64 
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-64-1679 TCGA-64-5774 
       39.25        40.96        29.92        56.81        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        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 
       14.01        13.45         4.24        19.43         8.42        23.38 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6214 
       50.33        66.64        77.85        43.82        85.15        36.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
      100.57       163.10        27.16         5.69        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7159 
       21.90        39.95       119.51        19.50        32.09        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
       22.92         9.57       104.19       238.29        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 
       32.78        19.89        35.24        37.74         4.57        24.33 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       32.65        31.04        31.20        21.47        14.60        11.61 
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-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 
       26.47        10.62        41.36         1.97        10.19        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-95-7567 
       19.82        22.45        17.46        23.61         1.08        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       12.39        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-A4M0 TCGA-97-A4M5 
        5.39        18.12        15.39        14.30        21.44        20.84 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
       24.56        34.85        36.76         1.45        21.57        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 
       35.47        32.48        19.00        14.30        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4TE 
       86.14        49.35        37.35        86.04         5.49        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 
       74.33         0.13         1.64        47.08         0.49         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  EGFR MUTATED EGFR WILD-TYPE 
          0.36           0.00 
  EGFR MUTATED EGFR WILD-TYPE 
        108.66         238.29 
  EGFR MUTATED EGFR WILD-TYPE 
         20.68          21.52 
[1] "0.4 - 108.7 (20.7)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.3"
D4V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  EGFR MUTATED         2       15       13         6        12         10
  EGFR WILD-TYPE       2      106      119        40        54         60
                vv
clus             STAGE IIIB STAGE IV
  EGFR MUTATED            3        5
  EGFR WILD-TYPE          8       19
D4V3, multiclass
            clus
vv           EGFR MUTATED EGFR WILD-TYPE
  STAGE I               2              2
  STAGE IA             15            106
  STAGE IB             13            119
  STAGE IIA             6             40
  STAGE IIB            12             54
  STAGE IIIA           10             60
  STAGE IIIB            3              8
  STAGE IV              5             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 133 228  36  15
D4V4, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  T1           23            133
  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 270  77    58
D4V5, multiclass
       clus
vv      EGFR MUTATED EGFR WILD-TYPE
  N0              38            270
  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 216 198
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     44   23
  EGFR WILD-TYPE  216  198
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  FEMALE           44            216
  MALE             23            198
[1] 2 2
[1] FALSE
D4V8, binary
                cls
clus               0   1
  EGFR MUTATED    50  10
  EGFR WILD-TYPE 334  45
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     50   10
  EGFR WILD-TYPE  334   45
     clus
vv    EGFR MUTATED EGFR WILD-TYPE
  NO            50            334
  YES           10             45
[1] 2 2
[1] FALSE
D4V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  EGFR MUTATED                            2                                19
  EGFR WILD-TYPE                         15                                83
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  EGFR MUTATED                                                   39
  EGFR WILD-TYPE                                                257
                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                                    2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            19
  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)            257
  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 270  10   3  22
D4V13, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  R0           42            270
  R1            2             10
  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                        27   326
D4V14, multiclass
                                  clus
vv                                 EGFR MUTATED EGFR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              4
  BLACK OR AFRICAN AMERICAN                   3             27
  WHITE                                      52            326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V15, binary
                cls
clus               0   1
  EGFR MUTATED     0  51
  EGFR WILD-TYPE   6 300
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      0   51
  EGFR WILD-TYPE    6  300
                        clus
vv                       EGFR MUTATED EGFR WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           51            300
[1] 2 2
[1] FALSE

Clustering(5) Variable = STK11 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  STK11 MUTATED    43  33
  STK11 WILD-TYPE 255 138
  STK11 MUTATED STK11 WILD-TYPE 
             76             393 
  STK11 MUTATED STK11 WILD-TYPE 
             33             138 
$`STK11 MUTATED`
TCGA-44-6776 TCGA-44-7671 TCGA-44-A47F TCGA-50-5932 TCGA-55-8203 TCGA-55-A492 
       86.01        29.23        11.08        40.60        17.98        19.59 
TCGA-73-7498 TCGA-78-7166 TCGA-97-A4M3 TCGA-J2-8194 TCGA-MP-A4TD TCGA-05-4395 
       39.09         8.48        17.75        23.80        10.09         0.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4432 TCGA-05-5425 TCGA-44-6144 
        2.99        14.96        12.00        25.02        29.00        23.77 
TCGA-44-6779 TCGA-44-8120 TCGA-44-A479 TCGA-49-4486 TCGA-49-4487 TCGA-49-4507 
       16.44         8.55        15.98        76.21        28.11         8.81 
TCGA-50-5072 TCGA-50-5939 TCGA-53-7813 TCGA-55-6970 TCGA-55-6983 TCGA-55-7574 
        8.22        15.12        13.94        15.25        92.81        32.71 
TCGA-55-7913 TCGA-55-8092 TCGA-55-8299 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
       18.44         5.06        15.42        14.47        13.74        20.28 
TCGA-55-8615 TCGA-62-A46P TCGA-62-A46S TCGA-62-A470 TCGA-62-A471 TCGA-64-5774 
       14.66        19.53        54.35        39.25        40.96        87.98 
TCGA-69-7763 TCGA-73-4670 TCGA-73-4677 TCGA-75-5146 TCGA-75-6206 TCGA-78-7148 
       22.68         4.31         1.25        77.85        85.15        20.58 
TCGA-78-7152 TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7167 
       39.95        32.09        64.90        22.92         9.57        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-80-5608 TCGA-86-7701 
       26.53        31.20         8.02        53.33        93.11        31.13 
TCGA-86-7713 TCGA-86-8054 TCGA-86-8280 TCGA-86-8359 TCGA-91-6849 TCGA-95-A4VP 
       38.04        37.74        23.05        14.60         1.15        19.89 
TCGA-97-8179 TCGA-99-8025 TCGA-99-8032 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       14.30        34.85         1.45        29.46        11.05        24.36 
TCGA-NJ-A4YF TCGA-NJ-A4YP TCGA-NJ-A55O TCGA-NJ-A55R 
       71.05         1.64         0.43        19.82 

$`STK11 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-7661 
       14.73        26.30        38.10        23.93        27.78        18.31 
TCGA-44-7670 TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 
       29.00         9.37        46.72        16.04        17.16        11.64 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 
       21.47        41.69        23.05        48.62         5.79         7.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 
        7.99        16.01        23.18        14.53        21.44         6.15 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 
       19.66        19.73        16.93        19.69        32.12        18.15 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 
       13.68        16.93        22.65        20.58        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       13.87        52.60        82.68        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       13.71        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M7 TCGA-J2-8192 TCGA-L9-A443 TCGA-L9-A444 
       20.19        20.52        20.68        24.30         6.35        10.09 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4250 
       27.19         5.29        31.23         2.43        50.07         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4420 
       45.01        37.02        24.03        47.05        19.00        29.98 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 
       30.02        21.99        26.01        25.02        24.00         4.96 
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-38-4632 TCGA-38-A44F 
       97.74       120.79        37.71        49.05        44.61         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       46.98        44.42        42.77        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 
       33.73        26.56        33.30        28.37        28.01        19.56 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 
       23.15        21.63        23.18        32.45        61.28        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       19.46         7.17        36.07        18.87        23.64        12.66 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4488 
       15.32         9.44        11.54        13.64        13.45        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 
       12.66        35.54        14.07        32.84        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       55.89        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-50-5930 
      101.72        15.72        60.16        47.41        49.28         9.27 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       14.27        78.67         8.45        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       53.16        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       34.29        30.54        35.21        30.58        14.30        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
        5.62        42.51        40.73        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       69.34        45.34        32.71        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7576 
       70.26        31.30        28.67        20.02        27.09        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        3.91        23.15        25.41        15.39        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       34.19        17.65        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
       23.08        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
       17.56        15.72         0.36        17.72        19.96        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.10        17.62         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        3.25         0.92        15.81        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-64-1679 
       67.96        72.30        13.61        29.92        56.81        81.80 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       38.37         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-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.64         6.12        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41        13.41        13.51        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       19.43         8.42         6.90        23.38        26.30        15.35 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-75-5125 TCGA-75-5147 TCGA-75-6212 
       30.31         9.24        50.33        66.64        43.82        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       36.66       108.66       100.57       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       19.27       129.53        21.90       119.51        19.50        38.50 
TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
        5.88       104.19       238.29        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
      232.18        39.75        77.59       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        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 TCGA-91-8497 
        2.60        12.23        27.68         7.36        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.18        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
       19.00        41.82        18.67        12.39        27.29         2.76 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       42.25        64.60        63.52        61.48        25.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59        15.91        18.67         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       16.41        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE 
       18.67        24.56        36.76        21.57        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       32.48        19.00        14.30        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI 
       41.59        14.10        19.13        73.91        74.33         0.13 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-O1-A52J 
       47.08         0.49        59.11 

  STK11 MUTATED STK11 WILD-TYPE 
           0.00            0.13 
  STK11 MUTATED STK11 WILD-TYPE 
          93.11          238.29 
  STK11 MUTATED STK11 WILD-TYPE 
         20.085          21.570 
[1] "0.0 - 93.1 (20.1)"  "0.1 - 238.3 (21.6)"
[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      102      114        40        53         58
                 vv
clus              STAGE IIIB STAGE IV
  STK11 MUTATED            3        5
  STK11 WILD-TYPE          8       19
D5V3, multiclass
            clus
vv           STK11 MUTATED STK11 WILD-TYPE
  STAGE I                0               4
  STAGE IA              19             102
  STAGE IB              18             114
  STAGE IIA              6              40
  STAGE IIB             13              53
  STAGE IIIA            12              58
  STAGE IIIB             3               8
  STAGE IV               5              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
  STK11 MUTATED    21  44   7   5
  STK11 WILD-TYPE 135 217  36  13
D5V4, multiclass
    clus
vv   STK11 MUTATED STK11 WILD-TYPE
  T1            21             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    48  14    14
  STK11 WILD-TYPE 260  75    58
D5V5, multiclass
       clus
vv      STK11 MUTATED STK11 WILD-TYPE
  N0               48             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    31  46
  STK11 WILD-TYPE 229 175
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED     31   46
  STK11 WILD-TYPE  229  175
        clus
vv       STK11 MUTATED STK11 WILD-TYPE
  FEMALE            31             229
  MALE              46             175
[1] 2 2
[1] FALSE
D5V8, binary
                 cls
clus                0   1
  STK11 MUTATED    63  10
  STK11 WILD-TYPE 321  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED     63   10
  STK11 WILD-TYPE  321   45
     clus
vv    STK11 MUTATED STK11 WILD-TYPE
  NO             63             321
  YES            10              45
[1] 2 2
[1] FALSE
D5V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  STK11 MUTATED                            4                                21
  STK11 WILD-TYPE                         13                                81
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  STK11 MUTATED                                                   42
  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)            42
  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                                      13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               81
  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    52   3   0   3
  STK11 WILD-TYPE 260   9   4  22
D5V13, multiclass
    clus
vv   STK11 MUTATED STK11 WILD-TYPE
  R0            52             260
  R1             3               9
  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                           8    58
  STK11 WILD-TYPE                        22   320
D5V14, multiclass
                                  clus
vv                                 STK11 MUTATED STK11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    8              22
  WHITE                                       58             320
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V15, binary
                 cls
clus                0   1
  STK11 MUTATED     0  50
  STK11 WILD-TYPE   6 301
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK11 MUTATED      0   50
  STK11 WILD-TYPE    6  301
                        clus
vv                       STK11 MUTATED STK11 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            50             301
[1] 2 2
[1] FALSE

Clustering(6) Variable = RBM10 MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2               0   1
  RBM10 MUTATED    18  15
  RBM10 WILD-TYPE 280 156
  RBM10 MUTATED RBM10 WILD-TYPE 
             33             436 
  RBM10 MUTATED RBM10 WILD-TYPE 
             15             156 
$`RBM10 MUTATED`
TCGA-05-4418 TCGA-44-7661 TCGA-55-8090 TCGA-55-8205 TCGA-55-A491 TCGA-73-7498 
        9.01        18.31        19.66        19.69        20.58        39.09 
TCGA-78-7166 TCGA-97-A4M7 TCGA-05-4395 TCGA-05-4403 TCGA-05-4424 TCGA-44-7659 
        8.48        20.68         0.00        19.00        30.02        22.72 
TCGA-44-A47A TCGA-49-4494 TCGA-55-6983 TCGA-55-7281 TCGA-55-7727 TCGA-55-7815 
       15.32        35.54        92.81        28.67         3.91        25.41 
TCGA-55-8208 TCGA-55-8620 TCGA-55-A490 TCGA-62-A472 TCGA-64-1676 TCGA-64-5775 
       22.16        12.33         3.25        29.92        56.81         2.04 
TCGA-69-8254 TCGA-75-6214 TCGA-78-7148 TCGA-78-7158 TCGA-78-7220 TCGA-78-7537 
       13.45        36.66        20.58         5.88        26.53        53.33 
TCGA-91-6828 TCGA-91-6848 TCGA-MP-A4SW 
       10.62         7.36        58.45 

$`RBM10 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4427 
       19.96        14.01         9.96         8.02        20.05        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7670 
       26.30        38.10        23.93        27.78        86.01        29.00 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       29.23         9.37        11.08        46.72        16.04        17.16 
TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 
       11.64        40.60        21.47        41.69        23.05        48.62 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        5.79         7.79         7.99        16.01        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8207 
       21.44         6.15        19.73        17.98        16.93        32.12 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF 
       18.15        13.68        16.93        22.65        19.59        20.19 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-78-7633 TCGA-78-8660 
       20.65        13.87        52.60        82.68        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8192 TCGA-J2-8194 
       17.92        20.19        20.52        17.75        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        10.09        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4397 
       10.09        50.07         3.98        45.01        37.02        24.03 
TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
       47.05         2.99        14.96        29.98        12.00        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       26.01        25.02        25.02        24.00         4.96        29.00 
TCGA-05-5428 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-38-4632 TCGA-38-A44F 
       97.74       120.79        37.71        49.05        44.61         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       46.98        44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       19.56        23.15        21.63        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       16.44        19.46         7.17        36.07        18.87        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
       12.66         8.55        15.98         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 
       13.45        76.21        28.11        28.57        12.66        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       55.33        22.26        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       53.16        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 
       34.29        30.54        13.94        35.21        30.58        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       80.52         5.62        42.51        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6984 
       53.65         3.88        69.34        45.34        32.71        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7283 TCGA-55-7570 
       40.54       107.21        70.26        31.30        20.02        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7728 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
       32.71        22.03        23.15        15.39        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       34.19        17.65        18.44        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       15.19        23.08         5.06        17.79        23.64        15.65 
TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       29.19        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       13.74        20.28        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A493 
       17.62        14.66         1.58        20.71        21.40         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        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-64-1679 
       67.96        72.30        13.61        39.25        40.96        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       38.37        87.98        42.90        28.41        51.25        28.47 
TCGA-67-3771 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-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 
        6.05         4.41        13.41        13.51        14.01         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       19.43         8.42         6.90        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 
        4.31        30.31         9.24         1.25        50.33        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 
       77.85        43.82        85.15        49.84       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 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-78-8640 TCGA-78-8648 
        8.02        26.01        39.35        10.55       232.18        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59       110.50        93.11        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        38.04        20.55        32.78        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       35.24        37.74         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       22.82        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60        11.61        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       28.34        26.50        29.46        24.23        13.64        26.47 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
       41.36         1.97        10.19         2.60        12.23        27.68 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 
       17.46        23.61         1.08        19.00        41.82        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       12.39        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       21.60        20.58        21.44        19.76        20.84        18.67 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
       24.56        34.85        36.76         1.45        21.57        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 
       35.47        32.48        19.00        14.30        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       86.14        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       41.59        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.49         0.43        19.82        59.11 

  RBM10 MUTATED RBM10 WILD-TYPE 
           0.00            0.13 
  RBM10 MUTATED RBM10 WILD-TYPE 
          92.81          238.29 
  RBM10 MUTATED RBM10 WILD-TYPE 
         20.580          21.585 
[1] "0.0 - 92.8 (20.6)"  "0.1 - 238.3 (21.6)"
[1] "hr=" "1.5"
D6V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  RBM10 MUTATED         0        9        5         2         6          7
  RBM10 WILD-TYPE       4      112      127        44        60         63
                 vv
clus              STAGE IIIB STAGE IV
  RBM10 MUTATED            2        1
  RBM10 WILD-TYPE          9       23
D6V3, multiclass
            clus
vv           RBM10 MUTATED RBM10 WILD-TYPE
  STAGE I                0               4
  STAGE IA               9             112
  STAGE IB               5             127
  STAGE IIA              2              44
  STAGE IIB              6              60
  STAGE IIIA             7              63
  STAGE IIIB             2               9
  STAGE IV               1              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
  RBM10 MUTATED    11  15   4   3
  RBM10 WILD-TYPE 145 246  39  15
D6V4, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  T1            11             145
  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 289  84    64
D6V5, multiclass
       clus
vv      RBM10 MUTATED RBM10 WILD-TYPE
  N0               19             289
  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 250 198
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED     10   23
  RBM10 WILD-TYPE  250  198
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  FEMALE            10             250
  MALE              23             198
[1] 2 2
[1] FALSE
D6V8, binary
                 cls
clus                0   1
  RBM10 MUTATED    25   4
  RBM10 WILD-TYPE 359  51
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED     25    4
  RBM10 WILD-TYPE  359   51
     clus
vv    RBM10 MUTATED RBM10 WILD-TYPE
  NO             25             359
  YES             4              51
[1] 2 2
[1] FALSE
D6V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RBM10 MUTATED                            0                                10
  RBM10 WILD-TYPE                         17                                92
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RBM10 MUTATED                                                   21
  RBM10 WILD-TYPE                                                275
                 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                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               92
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             275
  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 285  10   4  25
D6V13, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  R0            27             285
  R1             2              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
  RBM10 MUTATED                                  0     0
  RBM10 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBM10 MUTATED                           0    26
  RBM10 WILD-TYPE                        30   352
D6V14, multiclass
                                  clus
vv                                 RBM10 MUTATED RBM10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              30
  WHITE                                       26             352
[1] 4 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   6 331
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      0   20
  RBM10 WILD-TYPE    6  331
                        clus
vv                       RBM10 MUTATED RBM10 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            20             331
[1] 2 2
[1] FALSE

Clustering(7) Variable = RB1 MUTATION ANALYSIS
D7V1, survival
               sevent
clus2             0   1
  RB1 MUTATED    19   7
  RB1 WILD-TYPE 279 164
  RB1 MUTATED RB1 WILD-TYPE 
           26           443 
  RB1 MUTATED RB1 WILD-TYPE 
            7           164 
$`RB1 MUTATED`
TCGA-95-7562 TCGA-95-7947 TCGA-97-8172 TCGA-05-4397 TCGA-05-4415 TCGA-35-5375 
        2.86        15.68        17.92        24.03         2.99         8.68 
TCGA-44-6775 TCGA-44-7660 TCGA-44-7669 TCGA-55-6968 TCGA-55-8208 TCGA-55-A48Z 
       23.18        19.46        18.87        42.51        22.16        21.40 
TCGA-75-5147 TCGA-78-7143 TCGA-86-8056 TCGA-86-8074 TCGA-86-8358 TCGA-91-6828 
       43.82       163.10         4.57         0.79        21.47        10.62 
TCGA-91-6829 TCGA-91-6835 TCGA-91-6847 TCGA-93-A4JN TCGA-93-A4JP TCGA-97-7553 
       41.36         2.60        27.68        23.61        19.00        61.48 
TCGA-J2-A4AE TCGA-L4-A4E5 
       35.47        19.00 

$`RB1 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-A4LX 
       17.29        16.54        15.65        21.40        18.18        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       10.09        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 
       50.07         3.98        45.01        37.02         0.00        47.05 
TCGA-05-4403 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       19.00        14.96        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       26.01        25.02        25.02        24.00         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 
       22.03         9.04         2.04         7.40         5.98        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 
      120.79        37.71        49.05        44.61         4.37        46.98 
TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       44.42        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-44-6148 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.15        21.63        32.45        61.28        16.44        22.72 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
        7.17        36.07        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        48.46        60.72        57.53        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99        36.79        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       30.54        13.94        35.21        30.58        14.30        80.52 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
        5.62        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
      107.21        70.26        31.30        28.67        20.02        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
       32.71        22.03         3.91        23.15        25.41        15.39 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       18.64        11.28        34.19        17.65        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       29.23        29.72        15.19        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       23.64        15.65        29.19        15.42        17.56        15.72 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
       14.47         0.36        13.74        20.28        17.72        19.96 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
       26.01        17.10        17.62        14.66         1.58        12.33 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 
       20.71         3.25         0.92        15.81        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-64-1679 TCGA-64-1681 
       39.25        40.96        29.92        56.81        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-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         4.41        13.41        13.51        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 
        4.24        19.43         8.42         6.90        23.38        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-75-5125 TCGA-75-5146 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       66.64        77.85        85.15        49.84        36.66       108.66 
TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      100.57        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-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 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-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        4.08        24.33        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        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 
       26.47         1.97        10.19        12.23         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JO TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
        1.08        41.82        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 
       19.89        42.25        64.60        63.52        25.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59        15.91        18.67         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 
       21.57        18.08        32.48        14.30        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        5.49        41.59        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       47.08         0.49         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 
        20.43         21.57 
[1] "0.8 - 163.1 (20.4)" "0.0 - 238.3 (21.6)"
[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      115      124        43        65         68
               vv
clus            STAGE IIIB STAGE IV
  RB1 MUTATED            2        3
  RB1 WILD-TYPE          9       21
D7V3, multiclass
            clus
vv           RB1 MUTATED RB1 WILD-TYPE
  STAGE I              1             3
  STAGE IA             6           115
  STAGE IB             8           124
  STAGE IIA            3            43
  STAGE IIB            1            65
  STAGE IIIA           2            68
  STAGE IIIB           2             9
  STAGE IV             3            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
  RB1 MUTATED    11  12   0   2
  RB1 WILD-TYPE 145 249  43  16
D7V4, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  T1          11           145
  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 290  85    69
D7V5, multiclass
       clus
vv      RB1 MUTATED RB1 WILD-TYPE
  N0             18           290
  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 247 208
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     13   13
  RB1 WILD-TYPE  247  208
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE          13           247
  MALE            13           208
[1] 2 2
[1] FALSE
D7V8, binary
               cls
clus              0   1
  RB1 MUTATED    19   3
  RB1 WILD-TYPE 365  52
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     19    3
  RB1 WILD-TYPE  365   52
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO           19           365
  YES           3            52
[1] 2 2
[1] FALSE
D7V9, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RB1 MUTATED                            2                                 5
  RB1 WILD-TYPE                         15                                97
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RB1 MUTATED                                                   15
  RB1 WILD-TYPE                                                281
               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            15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            5            97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          15           281
  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 296  12   4  21
D7V13, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  R0          16           296
  R1           0            12
  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                        28   358
D7V14, multiclass
                                  clus
vv                                 RB1 MUTATED RB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             6
  BLACK OR AFRICAN AMERICAN                  2            28
  WHITE                                     20           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"
D7V15, binary
               cls
clus              0   1
  RB1 MUTATED     1  21
  RB1 WILD-TYPE   5 330
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      1   21
  RB1 WILD-TYPE    5  330
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               1             5
  NOT HISPANIC OR LATINO          21           330
[1] 2 2
[1] FALSE

Clustering(8) Variable = ARID1A MUTATION ANALYSIS
D8V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED    18  11
  ARID1A WILD-TYPE 280 160
  ARID1A MUTATED ARID1A WILD-TYPE 
              29              440 
  ARID1A MUTATED ARID1A WILD-TYPE 
              11              160 
$`ARID1A MUTATED`
TCGA-05-4382 TCGA-05-4427 TCGA-38-4631 TCGA-44-6147 TCGA-44-7670 TCGA-55-7725 
       19.96        26.01        11.64        27.78        29.00        14.53 
TCGA-55-7914 TCGA-MP-A4TC TCGA-05-4425 TCGA-05-5715 TCGA-44-7667 TCGA-55-5899 
        6.15         2.43        21.99         2.04        36.07        30.58 
TCGA-55-7815 TCGA-55-8089 TCGA-55-8097 TCGA-55-8208 TCGA-55-8299 TCGA-55-A490 
       25.41        23.08        15.65        22.16        15.42         3.25 
TCGA-64-1681 TCGA-67-3771 TCGA-78-7156 TCGA-78-7167 TCGA-86-8278 TCGA-91-6831 
       38.37        20.05        32.09        88.14        31.04        10.19 
TCGA-97-7938 TCGA-99-8025 TCGA-L4-A4E5 TCGA-MN-A4N4 TCGA-MP-A4TI 
        0.59        34.85        19.00        38.63        14.10 

$`ARID1A WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4434 
       14.01         9.96         8.02        20.05         9.01        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 
       15.02        28.41        35.28        14.73        26.30        38.10 
TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F 
       23.93        86.01        18.31        29.23         9.37        11.08 
TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 
       46.72        16.04        17.16        11.64        40.60        21.47 
TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 
       41.69        23.05        48.62         5.79         7.79         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       16.01        23.18        21.44        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       12.00        30.02        26.01        25.02        25.02        24.00 
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-38-4632 
        8.68        97.74       120.79        37.71        49.05        44.61 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
        4.37        46.98        44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       23.77        19.56        23.15        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 
       61.28        16.44        22.72        19.46         7.17        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         8.55        15.98        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 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-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 
       29.75        55.89        53.29        55.33        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47       101.72        15.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
        8.22         9.27        14.27        78.67         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       48.46        60.72        57.53        53.16        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05        12.16         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99        36.79        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       35.21        14.30        80.52         5.62        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       15.25        46.03        53.65         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       31.30        28.67        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        3.91        23.15        15.39        18.64        11.28        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 
        5.06        17.79        23.64        29.19        17.56        15.72 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
       14.47         0.36        13.74        20.28        17.72        19.96 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
       26.01        17.10        17.62        14.66         1.58        12.33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 
       20.71        21.40         0.92        15.81        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-64-1679 TCGA-64-5774 
       39.25        40.96        29.92        56.81        81.80        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 
        2.04        42.90        28.41        51.25        28.47        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
       14.04        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
       13.41        13.51        14.01        13.45         4.24        19.43 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        8.42         6.90        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       30.31         9.24         1.25        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 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-78-7220 
       64.90        22.92         9.57       104.19       238.29        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 
       24.33         0.79        22.82        32.65        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-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-91-6840 
       26.47        10.62        41.36         1.97         2.60        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45        17.46        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       41.82        18.67        12.39        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       42.25        64.60        63.52        61.48        25.48        18.54 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       15.91        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       14.30        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
       18.67        24.56        36.76         1.45        21.57        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       35.47        32.48        14.30         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       49.35        37.35        86.04        58.85         5.49        41.59 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-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 
       74.33         0.13         1.64        47.08         0.49         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 
          21.990           21.455 
[1] "0.6 - 88.1 (22.0)"  "0.0 - 238.3 (21.5)"
[1] "hr=" "1.4"
D8V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ARID1A MUTATED         1       10        5         4         3          3
  ARID1A WILD-TYPE       3      111      127        42        63         67
                  vv
clus               STAGE IIIB STAGE IV
  ARID1A MUTATED            0        3
  ARID1A WILD-TYPE         11       21
D8V3, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                 1                3
  STAGE IA               10              111
  STAGE IB                5              127
  STAGE IIA               4               42
  STAGE IIB               3               63
  STAGE IIIA              3               67
  STAGE IIIB              0               11
  STAGE IV                3               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
  ARID1A MUTATED    15  12   2   1
  ARID1A WILD-TYPE 141 249  41  17
D8V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1             15              141
  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 289  82    69
D8V5, multiclass
       clus
vv      ARID1A MUTATED ARID1A WILD-TYPE
  N0                19              289
  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 242 209
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     18   12
  ARID1A WILD-TYPE  242  209
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE             18              242
  MALE               12              209
[1] 2 2
[1] FALSE
D8V8, binary
                  cls
clus                 0   1
  ARID1A MUTATED    25   1
  ARID1A WILD-TYPE 359  54
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     25    1
  ARID1A WILD-TYPE  359   54
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO              25              359
  YES              1               54
[1] 2 2
[1] FALSE
D8V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ARID1A MUTATED                            0                                 5
  ARID1A WILD-TYPE                         17                                97
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ARID1A MUTATED                                                   23
  ARID1A WILD-TYPE                                                273
                  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                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              273
  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 287  11   4  25
D8V13, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0             25              287
  R1              1               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
  ARID1A MUTATED                                  0     0
  ARID1A WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED                           2    22
  ARID1A WILD-TYPE                        28   356
D8V14, multiclass
                                  clus
vv                                 ARID1A MUTATED ARID1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     2               28
  WHITE                                        22              356
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V15, binary
                  cls
clus                 0   1
  ARID1A MUTATED     1  21
  ARID1A WILD-TYPE   5 330
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      1   21
  ARID1A WILD-TYPE    5  330
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             21              330
[1] 2 2
[1] FALSE

Clustering(9) Variable = NF1 MUTATION ANALYSIS
D9V1, survival
               sevent
clus2             0   1
  NF1 MUTATED    34  20
  NF1 WILD-TYPE 264 151
  NF1 MUTATED NF1 WILD-TYPE 
           54           415 
  NF1 MUTATED NF1 WILD-TYPE 
           20           151 
$`NF1 MUTATED`
TCGA-38-4629 TCGA-38-4631 TCGA-44-8119 TCGA-55-1592 TCGA-55-7724 TCGA-55-8204 
       28.41        11.64         9.37        23.05        23.18        16.93 
TCGA-55-8205 TCGA-55-8621 TCGA-73-4658 TCGA-95-7043 TCGA-L9-A444 TCGA-05-4424 
       19.69        16.93        52.60        16.54        10.09        30.02 
TCGA-44-2656 TCGA-44-2657 TCGA-44-3918 TCGA-44-5644 TCGA-44-6144 TCGA-44-6775 
       46.98        44.42        34.06        28.37        23.77        23.18 
TCGA-44-7667 TCGA-49-4488 TCGA-49-6767 TCGA-50-5045 TCGA-50-5068 TCGA-50-5072 
       36.07        28.57        22.26        71.47        49.28         8.22 
TCGA-50-5946 TCGA-50-6593 TCGA-50-8457 TCGA-55-6971 TCGA-55-6975 TCGA-55-7907 
       53.16        11.05        36.99        46.03         3.88        11.28 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8089 TCGA-55-A4DG TCGA-62-A46S TCGA-64-1679 
       19.82        29.23        23.08        19.99        54.35        81.80 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 TCGA-73-4676 TCGA-78-7146 
       13.61         5.42         4.41        13.41         9.24         5.69 
TCGA-78-7535 TCGA-78-7542 TCGA-86-8073 TCGA-86-8279 TCGA-86-8669 TCGA-91-6829 
       31.20        10.55        24.33        31.20        30.84        41.36 
TCGA-95-7944 TCGA-97-7547 TCGA-97-7553 TCGA-L4-A4E5 TCGA-MP-A4SY TCGA-NJ-A55A 
       12.39        64.60        61.48        19.00        49.35         0.49 

$`NF1 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 
       26.01        15.02        15.02        35.28        14.73        26.30 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       38.10        23.93        27.78        86.01        18.31        29.00 
TCGA-44-7671 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 
       29.23        11.08        46.72        16.04        17.16        11.64 
TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 
       40.60        21.47        41.69        48.62         5.79         7.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 
        7.99        16.01        14.53        21.44         6.15        19.66 
TCGA-55-8091 TCGA-55-8203 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-A48X 
       19.73        17.98        32.12        18.15        13.68        22.65 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4662 
       20.58        19.59        20.19        20.65        13.87        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 
       39.09         8.48        50.24        10.55        85.32        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 
       16.18         1.45         6.12        17.29         2.86        15.68 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 
       15.65        21.40        18.18        17.92        20.19        20.52 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-MN-A4N1 
       17.75        20.68        24.30        23.80         6.35        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
        5.29        31.23         2.43        10.09        50.07         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
       45.01        37.02         0.00        24.03        47.05        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 
        2.99        14.96        29.98        12.00        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        24.00         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 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-38-4632 TCGA-38-A44F TCGA-44-2665 
      120.79        37.71        49.05        44.61         4.37        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 
       37.15        38.24        33.73        26.56        33.30        28.01 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       19.56        23.15        21.63        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       22.72        19.46         7.17        18.87        23.64        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
        8.55        15.98        15.32         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       13.45        76.21        28.11        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-50-5044 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       55.33        20.52       101.72        15.72        60.16        47.41 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        9.27        14.27        78.67         8.45        15.12        48.46 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 
       60.72        57.53        42.35         3.91        25.55        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        6.21         0.72        10.13        36.79        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       30.54        13.94        35.21        30.58        14.30        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6980 
        5.62        42.51        40.73        15.25        53.65        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
       70.26        31.30        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
       22.03         3.91        23.15        25.41        15.39        18.64 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 
       34.19        17.65        18.44        29.72        15.19         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       17.79        23.64        15.65        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       17.56        15.72        14.47         0.36        13.74        20.28 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
        1.58        12.33        20.71        21.40         3.25         0.92 
TCGA-55-A494 TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       15.81         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V 
       49.25        47.80        19.53        56.71        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1681 
       13.61        39.25        40.96        29.92        56.81        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-69-7973 TCGA-69-7974 TCGA-69-7980 
        6.64         6.12        22.68         7.56         6.05        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        19.43         8.42         6.90 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 
       23.38        26.30        15.35         4.31        30.31         1.25 
TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
       50.33        66.64        77.85        43.82        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 
       36.66       108.66       100.57       163.10        27.16        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 
      104.19       238.29        88.14        26.53         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       26.01        39.35       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 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-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.08         4.57         0.79        22.82        32.65        31.04 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 
       23.05        21.47        14.60        11.61        13.91        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
       26.47        10.62         1.97        10.19         2.60        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45        17.46        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 
       41.82        18.67        27.29         2.76        19.89        42.25 
TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       63.52        25.48        18.54         0.59        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       20.58        21.44        19.76        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE 
       34.85        36.76         1.45        21.57        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       32.48        14.30        38.63         2.76        86.14        58.45 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE 
       37.35        86.04        58.85         5.49        41.59        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-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-A55O TCGA-NJ-A55R 
       74.33         0.13         1.64        47.08         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  NF1 MUTATED NF1 WILD-TYPE 
         0.49          0.00 
  NF1 MUTATED NF1 WILD-TYPE 
        81.80        238.29 
  NF1 MUTATED NF1 WILD-TYPE 
        23.18         21.40 
[1] "0.5 - 81.8 (23.2)"  "0.0 - 238.3 (21.4)"
[1] "hr=" "1"  
D9V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  NF1 MUTATED         1       16       18         4        10          4
  NF1 WILD-TYPE       3      105      114        42        56         66
               vv
clus            STAGE IIIB STAGE IV
  NF1 MUTATED            0        0
  NF1 WILD-TYPE         11       24
D9V3, multiclass
            clus
vv           NF1 MUTATED NF1 WILD-TYPE
  STAGE I              1             3
  STAGE IA            16           105
  STAGE IB            18           114
  STAGE IIA            4            42
  STAGE IIB           10            56
  STAGE IIIA           4            66
  STAGE IIIB           0            11
  STAGE IV             0            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 138 231  37  17
D9V4, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  T1          18           138
  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 266  81    68
D9V5, multiclass
       clus
vv      NF1 MUTATED NF1 WILD-TYPE
  N0             42           266
  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 231 195
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     29   26
  NF1 WILD-TYPE  231  195
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE          29           231
  MALE            26           195
[1] 2 2
[1] FALSE
D9V8, binary
               cls
clus              0   1
  NF1 MUTATED    47   6
  NF1 WILD-TYPE 337  49
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     47    6
  NF1 WILD-TYPE  337   49
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO           47           337
  YES           6            49
[1] 2 2
[1] FALSE
D9V9, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NF1 MUTATED                            1                                10
  NF1 WILD-TYPE                         16                                92
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NF1 MUTATED                                                   39
  NF1 WILD-TYPE                                                257
               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            16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                           10            92
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          39           257
  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 278  11   4  23
D9V13, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  R0          34           278
  R1           1            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
  NF1 MUTATED                                  0     0
  NF1 WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF1 MUTATED                           3    50
  NF1 WILD-TYPE                        27   328
D9V14, multiclass
                                  clus
vv                                 NF1 MUTATED NF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  3            27
  WHITE                                     50           328
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V15, binary
               cls
clus              0   1
  NF1 MUTATED     1  46
  NF1 WILD-TYPE   5 305
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      1   46
  NF1 WILD-TYPE    5  305
                        clus
vv                       NF1 MUTATED NF1 WILD-TYPE
  HISPANIC OR LATINO               1             5
  NOT HISPANIC OR LATINO          46           305
[1] 2 2
[1] FALSE

Clustering(10) Variable = SMARCA4 MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  SMARCA4 MUTATED    21  16
  SMARCA4 WILD-TYPE 277 155
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               37               432 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               16               155 
$`SMARCA4 MUTATED`
TCGA-05-5420 TCGA-38-4631 TCGA-44-8119 TCGA-49-6742 TCGA-78-8660 TCGA-80-5611 
       15.02        11.64         9.37        16.04        10.55        85.32 
TCGA-MP-A4TA TCGA-05-4432 TCGA-35-5375 TCGA-44-2656 TCGA-44-8117 TCGA-44-A479 
       31.23        25.02         8.68        46.98        12.66        15.98 
TCGA-49-6767 TCGA-50-5072 TCGA-50-5930 TCGA-50-5936 TCGA-53-7624 TCGA-55-6543 
       22.26         8.22         9.27         8.45        34.29        14.30 
TCGA-55-6969 TCGA-55-6975 TCGA-55-8089 TCGA-55-A48Y TCGA-55-A48Z TCGA-62-A46O 
       40.73         3.88        23.08        20.71        21.40        47.80 
TCGA-67-3771 TCGA-69-7980 TCGA-69-8255 TCGA-78-7148 TCGA-78-8640 TCGA-86-7711 
       20.05        13.51         4.24        20.58       232.18        34.39 
TCGA-86-8585 TCGA-86-8674 TCGA-97-8175 TCGA-97-8176 TCGA-J2-A4AD TCGA-MP-A4SY 
       11.61        26.50        18.12        15.39        18.08        49.35 
TCGA-NJ-A4YQ 
       47.08 

$`SMARCA4 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 
       26.01        15.02        28.41        35.28        14.73        26.30 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       38.10        23.93        27.78        86.01        18.31        29.00 
TCGA-44-7671 TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 
       29.23        11.08        46.72        17.16        11.64        40.60 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 
       21.47        41.69        23.05        48.62         5.79         7.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 
        7.99        16.01        23.18        14.53        21.44         6.15 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 
       19.66        19.73        17.98        16.93        19.69        32.12 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 
       18.15        13.68        16.93        22.65        20.58        19.59 
TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 
       20.19        20.65        13.87        52.60        82.68        39.09 
TCGA-78-7166 TCGA-78-7633 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
        8.48        50.24        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       17.29        16.54         2.86        15.68        15.65        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       18.18        17.92        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 
       24.30        23.80         6.35        10.09        27.19         5.29 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       29.98        12.00        30.02        21.99        26.01        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 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-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       44.61         4.37        44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       23.77        19.56        23.15        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
       61.28        16.44        22.72        19.46         7.17        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       18.87        23.64         8.55        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       35.54        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       55.89        53.29        55.33        20.52        71.47       101.72 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5931 TCGA-50-5933 
       15.72        60.16        47.41        49.28        14.27        78.67 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
        3.91        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
       10.13        36.99        36.79        27.25        30.54        13.94 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6970 
       35.21        30.58        80.52         5.62        42.51        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       46.03        53.65        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26        31.30        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       20.02        27.09        32.71        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       25.41        15.39        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 
       18.44        19.82        29.23        29.72        15.19         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       17.79        23.64        15.65        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       17.56        15.72        14.47         0.36        13.74        20.28 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
        1.58        12.33         3.25         0.92        15.81        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-64-1679 TCGA-64-1681 
       39.25        40.96        29.92        56.81        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-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       18.84        14.04        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 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-A59K TCGA-71-6725 
        4.41        13.41        14.01        13.45        19.43         8.42 
TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        6.90        23.38        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
        9.24         1.25        50.33        66.64        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       85.15        49.84        36.66       108.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 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-78-7167 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-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59       110.50        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
        5.88        31.13        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-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       14.60        13.91        30.84        27.58         0.62        28.34 
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-91-6840 TCGA-91-6847 TCGA-91-6848 
        1.97        10.19         2.60        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 
       17.46        23.61         1.08        19.00        41.82        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       12.39        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.67         5.39        16.41        14.30        21.60        20.58 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       36.76         1.45        21.57        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
       14.30        38.63         2.76        86.14        58.45        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.13         1.64         0.49         0.43        19.82        59.11 

  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
             3.88              0.00 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
           232.18            238.29 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
           18.120            21.765 
[1] "3.9 - 232.2 (18.1)" "0.0 - 238.3 (21.8)"
[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      113      123        41        59         64
                   vv
clus                STAGE IIIB STAGE IV
  SMARCA4 MUTATED            1        1
  SMARCA4 WILD-TYPE         10       23
D10V3, multiclass
            clus
vv           SMARCA4 MUTATED SMARCA4 WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                 8               113
  STAGE IB                 9               123
  STAGE IIA                5                41
  STAGE IIB                7                59
  STAGE IIIA               6                64
  STAGE IIIB               1                10
  STAGE IV                 1                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
  SMARCA4 MUTATED    11  24   3   0
  SMARCA4 WILD-TYPE 145 237  40  18
D10V4, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  T1              11               145
  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 287  79    66
D10V5, multiclass
       clus
vv      SMARCA4 MUTATED SMARCA4 WILD-TYPE
  N0                 21               287
  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 246 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     14   24
  SMARCA4 WILD-TYPE  246  197
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  FEMALE              14               246
  MALE                24               197
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED    27   5
  SMARCA4 WILD-TYPE 357  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     27    5
  SMARCA4 WILD-TYPE  357   50
     clus
vv    SMARCA4 MUTATED SMARCA4 WILD-TYPE
  NO               27               357
  YES               5                50
[1] 2 2
[1] FALSE
D10V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  SMARCA4 MUTATED                            1
  SMARCA4 WILD-TYPE                         16
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  SMARCA4 MUTATED                                   5
  SMARCA4 WILD-TYPE                                97
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SMARCA4 MUTATED                                                   24
  SMARCA4 WILD-TYPE                                                272
                   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                                        16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               272
  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 289  12   4  23
D10V13, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  R0              23               289
  R1               0                12
  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                        28   347
D10V14, multiclass
                                  clus
vv                                 SMARCA4 MUTATED SMARCA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      2                28
  WHITE                                         31               347
[1] 4 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   3 325
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED      3   26
  SMARCA4 WILD-TYPE    3  325
                        clus
vv                       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  HISPANIC OR LATINO                   3                 3
  NOT HISPANIC OR LATINO              26               325
[1] 2 2
[1] FALSE

Clustering(11) Variable = BRAF MUTATION ANALYSIS
D11V1, survival
                sevent
clus2              0   1
  BRAF MUTATED    25  12
  BRAF WILD-TYPE 273 159
  BRAF MUTATED BRAF WILD-TYPE 
            37            432 
  BRAF MUTATED BRAF WILD-TYPE 
            12            159 
$`BRAF MUTATED`
TCGA-05-4382 TCGA-55-6979 TCGA-55-8511 TCGA-78-7633 TCGA-78-8660 TCGA-97-A4M7 
       19.96         7.79        18.15        50.24        10.55        20.68 
TCGA-MN-A4N1 TCGA-05-4249 TCGA-05-4389 TCGA-05-5428 TCGA-44-2656 TCGA-44-3918 
       27.19        50.07        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        48.46        60.72        53.16 
TCGA-50-6594 TCGA-53-A4EZ TCGA-55-6968 TCGA-55-7903 TCGA-55-7913 TCGA-55-8092 
       12.16        35.21        42.51        18.64        18.44         5.06 
TCGA-55-8506 TCGA-62-A46V TCGA-62-A472 TCGA-69-7765 TCGA-75-5146 TCGA-78-7153 
        0.36        72.30        29.92         5.42        77.85       119.51 
TCGA-78-7537 TCGA-78-7539 TCGA-78-8662 TCGA-86-7714 TCGA-91-A4BD TCGA-95-7039 
       53.33        26.01       110.50        20.55        19.82        41.82 
TCGA-L4-A4E6 
       14.30 

$`BRAF WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       14.01         9.96         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
       48.62         5.79         7.99        16.01        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       21.44         6.15        19.66        19.73        17.98        16.93 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 
       19.69        32.12        13.68        16.93        22.65        20.58 
TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       19.59        20.19        20.65        13.87        52.60        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
       39.09         8.48        85.32        13.71        16.18         1.45 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
        6.12        17.29        16.54         2.86        15.68        15.65 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       21.40        18.18        17.92        20.19        20.52        17.75 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MP-A4T8 TCGA-MP-A4TA 
       24.30        23.80         6.35        10.09         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
        2.43        10.09         3.98        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       47.05        19.00         2.99        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 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-38-4632 
        8.68        97.74       120.79        37.71        49.05        44.61 
TCGA-38-A44F TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 
        4.37        44.42        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-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.15        23.18        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       19.46         7.17        36.07        18.87        23.64        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
        8.55        15.98        15.32         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       53.29        55.33        22.26        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 
       60.16        47.41        49.28         8.22        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
        8.45        15.12        57.53        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       11.05         6.21         0.72        10.13        36.99        36.79 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-5899 TCGA-55-6543 
       27.25        34.29        30.54        13.94        30.58        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
       80.52         5.62        40.73        15.25        46.03        53.65 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26        31.30        28.67        20.02 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       27.09        32.71        22.03         3.91        23.15        25.41 
TCGA-55-7816 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 
       15.39        11.28        34.19        17.65        19.82        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       29.72        15.19        23.08        17.79        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       29.19        22.16        15.42        17.56        15.72        14.47 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       13.74        20.28        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.62        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        3.25         0.92        15.81        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 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-A46Y TCGA-62-A470 TCGA-62-A471 
       56.71        54.35        67.96        13.61        39.25        40.96 
TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       56.81        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-69-7760 TCGA-69-7761 TCGA-69-7763 
       14.73         5.72         4.64         6.64         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        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        19.43         8.42         6.90 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       23.38        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
        1.25        50.33        66.64        43.82        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       36.66       108.66       100.57       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 
       19.27        20.58       129.53        21.90        39.95        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      104.19       238.29        88.14        26.53        31.20         8.02 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 
       39.35        10.55       232.18        39.75        77.59        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        38.04 
TCGA-86-7953 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        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
       14.27         1.18        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       19.00        18.67        12.39        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       42.25        64.60        63.52        61.48        25.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59        15.91        18.67         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-MN-A4N4 
       21.57        18.08        35.47        32.48        19.00        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.85         5.49        41.59        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        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        47.08         0.49         0.43        19.82        59.11 

  BRAF MUTATED BRAF WILD-TYPE 
          0.36           0.00 
  BRAF MUTATED BRAF WILD-TYPE 
        119.51         238.29 
  BRAF MUTATED BRAF WILD-TYPE 
         26.01          21.42 
[1] "0.4 - 119.5 (26.0)" "0.0 - 238.3 (21.4)"
[1] "hr=" "1.5"
D11V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  BRAF MUTATED         0        8       11         5         7          5
  BRAF WILD-TYPE       4      113      121        41        59         65
                vv
clus             STAGE IIIB STAGE IV
  BRAF MUTATED            1        1
  BRAF WILD-TYPE         10       23
D11V3, multiclass
            clus
vv           BRAF MUTATED BRAF WILD-TYPE
  STAGE I               0              4
  STAGE IA              8            113
  STAGE IB             11            121
  STAGE IIA             5             41
  STAGE IIB             7             59
  STAGE IIIA            5             65
  STAGE IIIB            1             10
  STAGE IV              1             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    13  19   5   2
  BRAF WILD-TYPE 143 242  38  16
D11V4, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  T1           13            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    26   8     5
  BRAF WILD-TYPE 282  81    67
D11V5, multiclass
       clus
vv      BRAF MUTATED BRAF WILD-TYPE
  N0              26            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    17  22
  BRAF WILD-TYPE 243 199
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     17   22
  BRAF WILD-TYPE  243  199
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE           17            243
  MALE             22            199
[1] 2 2
[1] FALSE
D11V8, binary
                cls
clus               0   1
  BRAF MUTATED    27   9
  BRAF WILD-TYPE 357  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     27    9
  BRAF WILD-TYPE  357   46
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO            27            357
  YES            9             46
[1] 2 2
[1] FALSE
D11V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  BRAF MUTATED                            1                                14
  BRAF WILD-TYPE                         16                                88
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  BRAF MUTATED                                                   24
  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)           24
  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                                     16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              88
  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    25   0   0   3
  BRAF WILD-TYPE 287  12   4  22
D11V13, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  R0           25            287
  R1            0             12
  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                           5    24
  BRAF WILD-TYPE                        25   354
D11V14, multiclass
                                  clus
vv                                 BRAF MUTATED BRAF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   5             25
  WHITE                                      24            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"
D11V15, binary
                cls
clus               0   1
  BRAF MUTATED     1  22
  BRAF WILD-TYPE   5 329
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      1   22
  BRAF WILD-TYPE    5  329
                        clus
vv                       BRAF MUTATED BRAF WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO           22            329
[1] 2 2
[1] FALSE

Clustering(12) Variable = MGA MUTATION ANALYSIS
D12V1, survival
               sevent
clus2             0   1
  MGA MUTATED    24  16
  MGA WILD-TYPE 274 155
  MGA MUTATED MGA WILD-TYPE 
           40           429 
  MGA MUTATED MGA WILD-TYPE 
           16           155 
$`MGA MUTATED`
TCGA-05-4405 TCGA-05-4418 TCGA-44-7670 TCGA-44-7671 TCGA-49-6745 TCGA-55-8511 
       20.05         9.01        29.00        29.23        17.16        18.15 
TCGA-93-A4JQ TCGA-95-7043 TCGA-97-A4LX TCGA-L9-A443 TCGA-L9-A444 TCGA-05-5428 
       17.29        16.54        20.19         6.35        10.09        22.03 
TCGA-05-5715 TCGA-35-5375 TCGA-38-4628 TCGA-44-5644 TCGA-44-8117 TCGA-44-A4SU 
        2.04         8.68        49.05        28.37        12.66        13.45 
TCGA-49-4494 TCGA-49-6743 TCGA-50-5931 TCGA-55-6712 TCGA-55-6968 TCGA-55-7574 
       35.54        53.29        14.27         5.62        42.51        32.71 
TCGA-55-7907 TCGA-55-8208 TCGA-55-8506 TCGA-55-A490 TCGA-64-5779 TCGA-69-7763 
       11.28        22.16         0.36         3.25        28.41        22.68 
TCGA-69-7974 TCGA-69-A59K TCGA-71-8520 TCGA-73-4668 TCGA-78-7156 TCGA-78-7220 
        6.05        19.43         6.90        15.35        32.09        26.53 
TCGA-86-7955 TCGA-91-6829 TCGA-91-A4BD TCGA-95-7039 
       35.24        41.36        19.82        41.82 

$`MGA WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4427 TCGA-05-4434 
       19.96        14.01         9.96         8.02        26.01        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       15.02        28.41        35.28        11.64        14.73        26.30 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-8119 
       38.10        23.93        27.78        86.01        18.31         9.37 
TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 
       11.08        46.72        16.04        11.64        40.60        21.47 
TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 
       41.69        23.05        48.62         5.79         7.79         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 
       16.01        23.18        14.53        21.44         6.15        19.66 
TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8619 
       19.73        17.98        16.93        19.69        32.12        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-MN-A4N1 
       20.52        17.75        20.68        24.30        23.80        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
        5.29        31.23         2.43        10.09        50.07         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
       45.01        37.02         0.00        24.03        47.05        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       26.01        25.02        25.02        24.00         4.96        29.00 
TCGA-05-5429 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        9.04         7.40         5.98        97.74       120.79        37.71 
TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 
       44.61         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-44-5645 
       38.24        34.06        33.73        26.56        33.30        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       23.77        19.56        23.15        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
       61.28        16.44        22.72        19.46         7.17        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       18.87        23.64         8.55        15.98        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       11.54        13.64        76.21        28.11        28.57        12.66 
TCGA-49-4505 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-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       55.33        22.26        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5933 
       60.16        47.41        49.28         8.22         9.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        48.46        60.72        57.53        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99        36.79        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       30.54        13.94        35.21        30.58        14.30        80.52 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       40.73        15.25        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7576 
       70.26        31.30        28.67        20.02        27.09        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 
        3.91        23.15        25.41        15.39        18.64        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       23.08         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
       15.42        17.56        15.72        14.47        13.74        20.28 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A493 TCGA-55-A494 
        1.58        12.33        20.71        21.40         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-64-1679 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-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        4.64         6.64         6.12        13.61         5.42         7.56 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41        13.41        13.51        14.01        13.45         4.24 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
        8.42        23.38        26.30         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
        1.25        50.33        66.64        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       49.84        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 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-78-7167 TCGA-78-7535 TCGA-78-7536 
        9.57       104.19       238.29        88.14        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
       53.33        26.01        39.35        10.55       232.18        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59       110.50        93.11        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        38.04        20.55        32.78        19.89 
TCGA-86-8054 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 
       11.61        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-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
        1.97        10.19         2.60        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-93-7347 TCGA-93-7348 
        1.15        16.60        14.27         1.18        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
       23.61         1.08        19.00        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       25.48        18.54         0.59        15.91        18.67         5.39 
TCGA-97-8175 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-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       36.76         1.45        21.57        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       19.00        14.30        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       49.35        37.35        86.04        58.85         5.49        41.59 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        24.36        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        74.33         0.13         1.64        47.08         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  MGA MUTATED MGA WILD-TYPE 
         0.36          0.00 
  MGA MUTATED MGA WILD-TYPE 
        53.29        238.29 
  MGA MUTATED MGA WILD-TYPE 
       19.625        21.600 
[1] "0.4 - 53.3 (19.6)"  "0.0 - 238.3 (21.6)"
[1] "hr=" "1.6"
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      114      120        40        61         62
               vv
clus            STAGE IIIB STAGE IV
  MGA MUTATED            0        2
  MGA WILD-TYPE         11       22
D12V3, multiclass
            clus
vv           MGA MUTATED MGA WILD-TYPE
  STAGE I              0             4
  STAGE IA             7           114
  STAGE IB            12           120
  STAGE IIA            6            40
  STAGE IIB            5            61
  STAGE IIIA           8            62
  STAGE IIIB           0            11
  STAGE IV             2            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
  MGA MUTATED    12  22   5   1
  MGA WILD-TYPE 144 239  38  17
D12V4, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  T1          12           144
  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 284  81    64
D12V5, multiclass
       clus
vv      MGA MUTATED MGA WILD-TYPE
  N0             24           284
  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 238 203
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     22   18
  MGA WILD-TYPE  238  203
        clus
vv       MGA MUTATED MGA WILD-TYPE
  FEMALE          22           238
  MALE            18           203
[1] 2 2
[1] FALSE
D12V8, binary
               cls
clus              0   1
  MGA MUTATED    27   8
  MGA WILD-TYPE 357  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     27    8
  MGA WILD-TYPE  357   47
     clus
vv    MGA MUTATED MGA WILD-TYPE
  NO           27           357
  YES           8            47
[1] 2 2
[1] FALSE
D12V9, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MGA MUTATED                            2                                12
  MGA WILD-TYPE                         15                                90
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MGA MUTATED                                                   23
  MGA WILD-TYPE                                                273
               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            15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                           12            90
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          23           273
  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   2   0   3
  MGA WILD-TYPE 290  10   4  22
D12V13, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  R0          22           290
  R1           2            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                        28   346
D12V14, multiclass
                                  clus
vv                                 MGA MUTATED MGA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           1             0
  ASIAN                                      1             6
  BLACK OR AFRICAN AMERICAN                  2            28
  WHITE                                     32           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"
D12V15, binary
               cls
clus              0   1
  MGA MUTATED     1  30
  MGA WILD-TYPE   5 321
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED      1   30
  MGA WILD-TYPE    5  321
                        clus
vv                       MGA MUTATED MGA WILD-TYPE
  HISPANIC OR LATINO               1             5
  NOT HISPANIC OR LATINO          30           321
[1] 2 2
[1] FALSE

Clustering(13) Variable = FTSJD1 MUTATION ANALYSIS
D13V1, survival
                  sevent
clus2                0   1
  FTSJD1 MUTATED    16   8
  FTSJD1 WILD-TYPE 282 163
  FTSJD1 MUTATED FTSJD1 WILD-TYPE 
              24              445 
  FTSJD1 MUTATED FTSJD1 WILD-TYPE 
               8              163 
$`FTSJD1 MUTATED`
TCGA-55-8511 TCGA-55-A491 TCGA-73-4658 TCGA-93-8067 TCGA-95-A4VN TCGA-05-4420 
       18.15        20.58        52.60         6.12        18.18        29.98 
TCGA-38-4625 TCGA-44-3398 TCGA-44-4112 TCGA-50-5930 TCGA-50-8457 TCGA-55-8206 
       97.74        38.24        26.56         9.27        36.99        29.19 
TCGA-55-8506 TCGA-55-8514 TCGA-55-A490 TCGA-64-1679 TCGA-78-7155 TCGA-78-8662 
        0.36        17.10         3.25        81.80        38.50       110.50 
TCGA-86-A4JF TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-MP-A4SV TCGA-MP-A4TH TCGA-NJ-A4YP 
       24.23        32.48        19.00        86.14        24.36         1.64 

$`FTSJD1 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 
       17.98        16.93        19.69        32.12        13.68        16.93 
TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4662 
       22.65        19.59        20.19        20.65        13.87        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 
       39.09         8.48        50.24        10.55        85.32        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 
       16.18         1.45        17.29        16.54         2.86        15.68 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       15.65        21.40        17.92        20.19        20.52        17.75 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       20.68        24.30        23.80         6.35        10.09        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
        5.29        31.23         2.43        10.09        50.07         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
       45.01        37.02         0.00        24.03        47.05        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        2.99        14.96        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        24.00         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 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-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       37.71        49.05        44.61         4.37        46.98        44.42 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 
       42.77        37.15        34.06        33.73        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       47.41        49.28         8.22        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
        3.91        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       10.13        36.79        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       35.21        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       40.73        15.25        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
       70.26        31.30        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
       22.03         3.91        23.15        25.41        15.39        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 
       11.28        34.19        17.65        18.44        19.82        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       29.72        15.19        23.08         5.06        17.79        23.64 
TCGA-55-8097 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       15.65        22.16        15.42        17.56        15.72        14.47 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
       13.74        20.28        17.72        19.96        26.01        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A493 
       14.66         1.58        12.33        20.71        21.40         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        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-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       56.81        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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        19.43         8.42         6.90 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       23.38        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
        1.25        50.33        66.64        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       49.84        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
      119.51        19.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        9.57       104.19       238.29        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       39.75        77.59        93.11        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        38.04        20.55        32.78        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       35.24        37.74         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       22.82        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60        11.61        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-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-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
        7.36         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       22.45        17.46        23.61         1.08        19.00        41.82 
TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 
       18.67        12.39        27.29         2.76        19.89        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        61.48        25.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       15.91        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       14.30        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW 
       18.08        35.47        14.30        38.63         2.76        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       49.35        37.35        86.04        58.85         5.49        41.59 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-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 
       74.33         0.13        47.08         0.49         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  FTSJD1 MUTATED FTSJD1 WILD-TYPE 
            0.36             0.00 
  FTSJD1 MUTATED FTSJD1 WILD-TYPE 
          110.50           238.29 
  FTSJD1 MUTATED FTSJD1 WILD-TYPE 
           25.46            21.44 
[1] "0.4 - 110.5 (25.5)" "0.0 - 238.3 (21.4)"
[1] "hr=" "1.3"
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      115      121        44        64         68
                  vv
clus               STAGE IIIB STAGE IV
  FTSJD1 MUTATED            0        0
  FTSJD1 WILD-TYPE         11       24
D13V3, multiclass
            clus
vv           FTSJD1 MUTATED FTSJD1 WILD-TYPE
  STAGE I                 1                3
  STAGE IA                6              115
  STAGE IB               11              121
  STAGE IIA               2               44
  STAGE IIB               2               64
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                0               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
  FTSJD1 MUTATED     8  14   2   0
  FTSJD1 WILD-TYPE 148 247  41  18
D13V4, multiclass
    clus
vv   FTSJD1 MUTATED FTSJD1 WILD-TYPE
  T1              8              148
  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 287  88    70
D13V5, multiclass
       clus
vv      FTSJD1 MUTATED FTSJD1 WILD-TYPE
  N0                21              287
  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 245 212
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FTSJD1 MUTATED     15    9
  FTSJD1 WILD-TYPE  245  212
        clus
vv       FTSJD1 MUTATED FTSJD1 WILD-TYPE
  FEMALE             15              245
  MALE                9              212
[1] 2 2
[1] FALSE
D13V8, binary
                  cls
clus                 0   1
  FTSJD1 MUTATED    21   1
  FTSJD1 WILD-TYPE 363  54
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FTSJD1 MUTATED     21    1
  FTSJD1 WILD-TYPE  363   54
     clus
vv    FTSJD1 MUTATED FTSJD1 WILD-TYPE
  NO              21              363
  YES              1               54
[1] 2 2
[1] FALSE
D13V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FTSJD1 MUTATED                            0                                 3
  FTSJD1 WILD-TYPE                         17                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FTSJD1 MUTATED                                                   19
  FTSJD1 WILD-TYPE                                                277
                  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                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              277
  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 292  12   4  24
D13V13, multiclass
    clus
vv   FTSJD1 MUTATED FTSJD1 WILD-TYPE
  R0             20              292
  R1              0               12
  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                        28   360
D13V14, multiclass
                                  clus
vv                                 FTSJD1 MUTATED FTSJD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     2               28
  WHITE                                        18              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"
D13V15, binary
                  cls
clus                 0   1
  FTSJD1 MUTATED     0  20
  FTSJD1 WILD-TYPE   6 331
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FTSJD1 MUTATED      0   20
  FTSJD1 WILD-TYPE    6  331
                        clus
vv                       FTSJD1 MUTATED FTSJD1 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             20              331
[1] 2 2
[1] FALSE

Clustering(14) Variable = MET MUTATION ANALYSIS
D14V1, survival
               sevent
clus2             0   1
  MET MUTATED    12   7
  MET WILD-TYPE 286 164
  MET MUTATED MET WILD-TYPE 
           19           450 
  MET MUTATED MET WILD-TYPE 
            7           164 
$`MET MUTATED`
TCGA-44-7671 TCGA-49-6745 TCGA-49-6761 TCGA-50-6597 TCGA-55-8511 TCGA-05-4403 
       29.23        17.16        11.64        41.69        18.15        19.00 
TCGA-44-2657 TCGA-44-A47G TCGA-50-5930 TCGA-50-5933 TCGA-55-6712 TCGA-55-6982 
       44.42        11.54         9.27        78.67         5.62        32.71 
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-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       18.31        29.00         9.37        11.08        46.72        16.04 
TCGA-50-5932 TCGA-50-5935 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 
       40.60        21.47        23.05        48.62         5.79         7.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 
        7.99        16.01        23.18        14.53        21.44         6.15 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 
       19.66        19.73        17.98        16.93        19.69        32.12 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF 
       13.68        16.93        22.65        20.58        19.59        20.19 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       20.65        13.87        52.60        82.68        39.09         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
       50.24        10.55        85.32        13.71        16.18         1.45 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
        6.12        17.29        16.54         2.86        15.68        15.65 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       21.40        18.18        17.92        20.19        20.52        17.75 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       20.68        24.30        23.80         6.35        10.09        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
        5.29        31.23         2.43        10.09        50.07         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4415 
       45.01        37.02         0.00        24.03        47.05         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        24.00         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 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-38-4632 TCGA-38-A44F TCGA-44-2656 
      120.79        37.71        49.05        44.61         4.37        46.98 
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-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       19.46         7.17        36.07        18.87        23.64        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A4SS TCGA-44-A4SU 
        8.55        15.98        15.32         9.44        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       55.33        22.26        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5936 
       60.16        47.41        49.28         8.22        14.27         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
        3.91        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99        36.79        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 
       13.94        35.21        30.58        14.30        80.52        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       40.73        15.25        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       45.34        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       31.30        28.67        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        3.91        23.15        25.41        15.39        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       34.19        17.65        18.44        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       15.19        23.08         5.06        17.79        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       29.19        22.16        15.42        17.56        15.72        14.47 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36        13.74        20.28        17.72        19.96        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
       17.10        17.62        14.66         1.58        12.33        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 
       21.40         3.25         0.92        15.81        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-64-1679 TCGA-64-1681 
       39.25        40.96        29.92        56.81        81.80        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 
       87.98         2.04        42.90        28.41        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       18.84        14.04        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41        13.41        13.51        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       19.43         8.42         6.90        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 
        4.31        30.31         9.24         1.25        50.33        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       77.85        43.82        85.15        49.84        36.66       108.66 
TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      100.57        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-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 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        11.61        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
       10.19         2.60        12.23         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JO 
       14.27         1.18        19.82        22.45        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
       19.00        41.82        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 
       21.57        18.08        32.48        19.00        14.30        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.85         5.49        41.59        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        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        47.08         0.49         0.43        19.82        59.11 

  MET MUTATED MET WILD-TYPE 
         5.62          0.00 
  MET MUTATED MET WILD-TYPE 
       163.10        238.29 
  MET MUTATED MET WILD-TYPE 
       21.470        21.455 
[1] "5.6 - 163.1 (21.5)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.2"
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      118      121        45        65         66
               vv
clus            STAGE IIIB STAGE IV
  MET MUTATED            1        0
  MET WILD-TYPE         10       24
D14V3, multiclass
            clus
vv           MET MUTATED MET WILD-TYPE
  STAGE I              0             4
  STAGE IA             3           118
  STAGE IB            11           121
  STAGE IIA            1            45
  STAGE IIB            1            65
  STAGE IIIA           4            66
  STAGE IIIB           1            10
  STAGE IV             0            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
  MET MUTATED     4  15   1   1
  MET WILD-TYPE 152 246  42  17
D14V4, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  T1           4           152
  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 295  86    68
D14V5, multiclass
       clus
vv      MET MUTATED MET WILD-TYPE
  N0             13           295
  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 248 212
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED     12    9
  MET WILD-TYPE  248  212
        clus
vv       MET MUTATED MET WILD-TYPE
  FEMALE          12           248
  MALE             9           212
[1] 2 2
[1] FALSE
D14V8, binary
               cls
clus              0   1
  MET MUTATED    16   4
  MET WILD-TYPE 368  51
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED     16    4
  MET WILD-TYPE  368   51
     clus
vv    MET MUTATED MET WILD-TYPE
  NO           16           368
  YES           4            51
[1] 2 2
[1] FALSE
D14V9, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MET MUTATED                            1                                 4
  MET WILD-TYPE                         16                                98
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MET MUTATED                                                   15
  MET WILD-TYPE                                                281
               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            16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            4            98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          15           281
  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   1   0   0
  MET WILD-TYPE 298  11   4  25
D14V13, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  R0          14           298
  R1           1            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                        29   361
D14V14, multiclass
                                  clus
vv                                 MET MUTATED MET WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  1            29
  WHITE                                     17           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"
D14V15, binary
               cls
clus              0   1
  MET MUTATED     0  14
  MET WILD-TYPE   6 337
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      0   14
  MET WILD-TYPE    6  337
                        clus
vv                       MET MUTATED MET WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO          14           337
[1] 2 2
[1] FALSE

Clustering(15) Variable = GAGE2A MUTATION ANALYSIS
D15V1, survival
                  sevent
clus2                0   1
  GAGE2A MUTATED     5   3
  GAGE2A WILD-TYPE 293 168
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               8              461 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               3              168 
$`GAGE2A MUTATED`
TCGA-44-6147 TCGA-44-7661 TCGA-55-1592 TCGA-44-2665 TCGA-44-3396 TCGA-44-6779 
       27.78        18.31        23.05        42.77        37.15        16.44 
TCGA-55-8302 TCGA-86-8674 
       15.72        26.50 

$`GAGE2A WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6776 TCGA-44-7670 
       14.73        26.30        38.10        23.93        86.01        29.00 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       29.23         9.37        11.08        46.72        16.04        17.16 
TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1595 TCGA-55-6978 
       11.64        40.60        21.47        41.69        48.62         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.79         7.99        16.01        23.18        14.53        21.44 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 
        6.15        19.66        19.73        17.98        16.93        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 
       32.12        18.15        13.68        16.93        22.65        20.58 
TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       19.59        20.19        20.65        13.87        52.60        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 
       39.09         8.48        50.24        10.55        85.32        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       16.18         1.45         6.12        17.29        16.54         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       15.68        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       10.09        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       47.05        19.00         2.99        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-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-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-3398 TCGA-44-3918 
       44.61         4.37        46.98        44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       19.56        23.15        21.63        23.18        32.45        61.28 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       22.72        19.46         7.17        36.07        18.87        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       12.66         8.55        15.98        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       35.54        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       55.89        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 
      101.72        15.72        60.16        47.41        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        9.27        14.27        78.67         8.45        15.12        48.46 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       60.72        57.53        53.16        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05        12.16         6.21         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.79        27.25        34.29        30.54        13.94        35.21 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       30.58        14.30        80.52         5.62        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       15.25        46.03        53.65         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       31.30        28.67        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        3.91        23.15        25.41        15.39        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       34.19        17.65        18.44        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       15.19        23.08         5.06        17.79        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 
       29.19        22.16        15.42        17.56        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       13.74        20.28        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.62        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        3.25         0.92        15.81        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 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-69-7760 
       18.84        14.04        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41        13.41        13.51        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       19.43         8.42         6.90        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 
        4.31        30.31         9.24         1.25        50.33        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       77.85        43.82        85.15        49.84        36.66       108.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
      100.57       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-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      238.29        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       26.01        39.35        10.55       232.18        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
      110.50        93.11        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 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 
       11.61        13.91        30.84        27.58         0.62        28.34 
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-91-6840 TCGA-91-6847 TCGA-91-6848 
        1.97        10.19         2.60        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 
       17.46        23.61         1.08        19.00        41.82        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       12.39        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       21.60        20.58        21.44        19.76        20.84        18.67 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
       24.56        34.85        36.76         1.45        21.57        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 
       35.47        32.48        19.00        14.30        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        5.49        41.59        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       47.08         0.49         0.43        19.82        59.11 

  GAGE2A MUTATED GAGE2A WILD-TYPE 
           15.72             0.00 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
           42.77           238.29 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
          24.775           21.440 
[1] "15.7 - 42.8 (24.8)" "0.0 - 238.3 (21.4)"
[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      119      130        45        64         69
                  vv
clus               STAGE IIIB STAGE IV
  GAGE2A MUTATED            0        0
  GAGE2A WILD-TYPE         11       24
D15V3, multiclass
            clus
vv           GAGE2A MUTATED GAGE2A WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              119
  STAGE IB                2              130
  STAGE IIA               1               45
  STAGE IIB               2               64
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               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
  GAGE2A MUTATED     1   7   0   0
  GAGE2A WILD-TYPE 155 254  43  18
D15V4, multiclass
    clus
vv   GAGE2A MUTATED GAGE2A WILD-TYPE
  T1              1              155
  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 305  86    71
D15V5, multiclass
       clus
vv      GAGE2A MUTATED GAGE2A WILD-TYPE
  N0                 3              305
  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 255 218
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      5    3
  GAGE2A WILD-TYPE  255  218
        clus
vv       GAGE2A MUTATED GAGE2A WILD-TYPE
  FEMALE              5              255
  MALE                3              218
[1] 2 2
[1] FALSE
D15V8, binary
                  cls
clus                 0   1
  GAGE2A MUTATED     8   0
  GAGE2A WILD-TYPE 376  55
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      8    0
  GAGE2A WILD-TYPE  376   55
     clus
vv    GAGE2A MUTATED GAGE2A WILD-TYPE
  NO               8              376
  YES              0               55
[1] 2 2
[1] FALSE
D15V9, continuous
[1] "Remove cluster labels:" "GAGE2A MUTATED"        
clus
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               2              120 
      TCGA-44-A47F       TCGA-49-6742       TCGA-55-7573       TCGA-55-7725 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8205       TCGA-55-8511       TCGA-55-8619 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-55-8621       TCGA-55-A491       TCGA-55-A492       TCGA-64-1677 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-73-4662       TCGA-73-7498       TCGA-93-8067       TCGA-MN-A4N1 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      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-49-4486       TCGA-49-4494       TCGA-49-4505       TCGA-49-4506 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-49-4510       TCGA-49-6743       TCGA-49-6744       TCGA-53-7624 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-53-A4EZ       TCGA-55-5899       TCGA-55-7283       TCGA-55-7574 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-55-7910       TCGA-55-7913       TCGA-55-7995       TCGA-55-8089 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-55-8096       TCGA-55-8208       TCGA-55-8507       TCGA-55-8508 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8513       TCGA-55-8620       TCGA-55-A48Z 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-55-A490       TCGA-55-A494       TCGA-62-8394       TCGA-62-8395 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-62-8397       TCGA-62-8398       TCGA-62-8399       TCGA-62-8402 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R       TCGA-62-A46S 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y       TCGA-62-A470 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-62-A471       TCGA-62-A472       TCGA-64-1681       TCGA-64-5775 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-64-5778       TCGA-69-7974       TCGA-69-8254       TCGA-71-6725 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-71-8520       TCGA-73-4659       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-73-7499 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-75-5122       TCGA-83-5908       TCGA-86-6562       TCGA-86-6851 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-86-7701       TCGA-86-7711       TCGA-86-7713       TCGA-86-7714 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-86-7953       TCGA-86-7954       TCGA-86-7955       TCGA-86-8054 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-86-8055       TCGA-86-8056       TCGA-86-8073       TCGA-86-8074 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-86-8075       TCGA-86-8076       TCGA-86-8278       TCGA-86-8279 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-86-8280       TCGA-86-8281       TCGA-86-8358       TCGA-86-8359 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-86-8668       TCGA-86-8669       TCGA-86-8671       TCGA-86-A456 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6829       TCGA-91-6849 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-93-7347       TCGA-93-7348       TCGA-93-A4JN       TCGA-93-A4JO 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-95-7567       TCGA-99-7458       TCGA-MN-A4N4       TCGA-MN-A4N5 
"GAGE2A WILD-TYPE" "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                         17                               102
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GAGE2A MUTATED                                                    7
  GAGE2A WILD-TYPE                                                289
                  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                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               102
  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"
D15V11, continuous
D15V12, continuous
                  vv
clus                R0  R1  R2  RX
  GAGE2A MUTATED     5   0   0   0
  GAGE2A WILD-TYPE 307  12   4  25
D15V13, multiclass
    clus
vv   GAGE2A MUTATED GAGE2A WILD-TYPE
  R0              5              307
  R1              0               12
  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                        30   370
D15V14, multiclass
                                  clus
vv                                 GAGE2A MUTATED GAGE2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               30
  WHITE                                         8              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"
D15V15, binary
                  cls
clus                 0   1
  GAGE2A MUTATED     0   6
  GAGE2A WILD-TYPE   6 345
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      0    6
  GAGE2A WILD-TYPE    6  345
                        clus
vv                       GAGE2A MUTATED GAGE2A WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              6              345
[1] 2 2
[1] FALSE

Clustering(16) Variable = SETD2 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2               0   1
  SETD2 MUTATED    16  12
  SETD2 WILD-TYPE 282 159
  SETD2 MUTATED SETD2 WILD-TYPE 
             28             441 
  SETD2 MUTATED SETD2 WILD-TYPE 
             12             159 
$`SETD2 MUTATED`
TCGA-05-4427 TCGA-38-4631 TCGA-55-8204 TCGA-55-A4DF TCGA-73-4658 TCGA-97-A4M7 
       26.01        11.64        16.93        20.19        52.60        20.68 
TCGA-05-4425 TCGA-49-4487 TCGA-49-6744 TCGA-50-5941 TCGA-50-5942 TCGA-53-7624 
       21.99        28.11        55.33        48.46        60.72        34.29 
TCGA-55-6986 TCGA-62-A46P TCGA-64-5775 TCGA-67-6216 TCGA-69-7760 TCGA-73-4666 
      107.21        19.53         2.04         4.64         6.64        26.30 
TCGA-73-4676 TCGA-75-6214 TCGA-75-7025 TCGA-78-7150 TCGA-86-7714 TCGA-86-8278 
        9.24        36.66       108.66        21.90        20.55        31.04 
TCGA-91-6848 TCGA-97-7941 TCGA-97-A4M6 TCGA-MP-A4SY 
        7.36        15.91        18.67        49.35 

$`SETD2 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 
       15.02        15.02        28.41        35.28        14.73        26.30 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       38.10        23.93        27.78        86.01        18.31        29.00 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       29.23         9.37        11.08        46.72        16.04        17.16 
TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 
       11.64        40.60        21.47        41.69        23.05        48.62 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        5.79         7.79         7.99        16.01        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8205 
       21.44         6.15        19.66        19.73        17.98        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 
       32.12        18.15        13.68        16.93        22.65        20.58 
TCGA-55-A492 TCGA-64-1677 TCGA-67-6217 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       19.59        20.65        13.87        82.68        39.09         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
       50.24        10.55        85.32        13.71        16.18         1.45 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
        6.12        17.29        16.54         2.86        15.68        15.65 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       21.40        18.18        17.92        20.19        20.52        17.75 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 
       24.30        23.80         6.35        10.09        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 
       31.23         2.43        10.09        50.07         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       37.02         0.00        24.03        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 TCGA-05-4430 
       14.96        29.98        12.00        30.02        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       25.02        24.00         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       37.71        49.05        44.61         4.37        46.98        44.42 
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-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       19.46         7.17        36.07        18.87        23.64        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
        8.55        15.98        15.32         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       13.45        76.21        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
        8.45        15.12        57.53        53.16        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05        12.16         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.99        36.79        27.25        30.54        13.94        35.21 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       30.58        14.30        80.52         5.62        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       15.25        46.03        53.65         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 TCGA-55-7227 
       32.71        92.81        24.99        40.54        70.26        31.30 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
       28.67        20.02        27.09        32.71        22.03         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
       23.15        25.41        15.39        18.64        11.28        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       23.08         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       13.74        20.28        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.62        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        3.25         0.92        15.81        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-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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 
       29.92        56.81        81.80        38.37        87.98        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-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       14.73         5.72         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        13.41        13.51        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 
       13.45         4.24        19.43         8.42         6.90        23.38 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 
       15.35         4.31        30.31         1.25        50.33        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7027 TCGA-78-7143 
       77.85        43.82        85.15        49.84       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 
       27.16         5.69        19.27        20.58       129.53        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
       22.92         9.57       104.19       238.29        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 
       12.36         5.88        31.13        34.39        38.04        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-86-8279 TCGA-86-8280 TCGA-86-8358 
        0.79        22.82        32.65        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60        11.61        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-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-91-6840 
       10.62        41.36         1.97        10.19         2.60        12.23 
TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
       27.68         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       22.45        17.46        23.61         1.08        19.00        41.82 
TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 
       18.67        12.39        27.29         2.76        19.89        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        61.48        25.48        18.54         0.59 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-99-7458 
       21.60        20.58        21.44        19.76        20.84        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE 
       34.85        36.76         1.45        21.57        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       32.48        19.00        14.30        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       58.45        37.35        86.04        58.85         5.49        41.59 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        24.36        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        74.33         0.13         1.64        47.08         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  SETD2 MUTATED SETD2 WILD-TYPE 
           2.04            0.00 
  SETD2 MUTATED SETD2 WILD-TYPE 
         108.66          238.29 
  SETD2 MUTATED SETD2 WILD-TYPE 
         21.945          21.440 
[1] "2.0 - 108.7 (21.9)" "0.0 - 238.3 (21.4)"
[1] "hr=" "1.1"
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      114      126        44        60         64
                 vv
clus              STAGE IIIB STAGE IV
  SETD2 MUTATED            0        3
  SETD2 WILD-TYPE         11       21
D16V3, multiclass
            clus
vv           SETD2 MUTATED SETD2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               7             114
  STAGE IB               6             126
  STAGE IIA              2              44
  STAGE IIB              6              60
  STAGE IIIA             6              64
  STAGE IIIB             0              11
  STAGE IV               3              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
  SETD2 MUTATED     9  18   2   1
  SETD2 WILD-TYPE 147 243  41  17
D16V4, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  T1             9             147
  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 290  82    67
D16V5, multiclass
       clus
vv      SETD2 MUTATED SETD2 WILD-TYPE
  N0               18             290
  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 240 211
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     20   10
  SETD2 WILD-TYPE  240  211
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  FEMALE            20             240
  MALE              10             211
[1] 2 2
[1] FALSE
D16V8, binary
                 cls
clus                0   1
  SETD2 MUTATED    25   4
  SETD2 WILD-TYPE 359  51
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     25    4
  SETD2 WILD-TYPE  359   51
     clus
vv    SETD2 MUTATED SETD2 WILD-TYPE
  NO             25             359
  YES             4              51
[1] 2 2
[1] FALSE
D16V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SETD2 MUTATED                            1                                 8
  SETD2 WILD-TYPE                         16                                94
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SETD2 MUTATED                                                   19
  SETD2 WILD-TYPE                                                277
                 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                                     1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              8
  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)             277
  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 289  11   3  25
D16V13, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  R0            23             289
  R1             1              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
  SETD2 MUTATED                                  0     0
  SETD2 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SETD2 MUTATED                           1    23
  SETD2 WILD-TYPE                        29   355
D16V14, multiclass
                                  clus
vv                                 SETD2 MUTATED SETD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              29
  WHITE                                       23             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"
D16V15, binary
                 cls
clus                0   1
  SETD2 MUTATED     1  19
  SETD2 WILD-TYPE   5 332
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      1   19
  SETD2 WILD-TYPE    5  332
                        clus
vv                       SETD2 MUTATED SETD2 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            19             332
[1] 2 2
[1] FALSE

Clustering(17) Variable = U2AF1 MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2               0   1
  U2AF1 MUTATED     8   3
  U2AF1 WILD-TYPE 290 168
  U2AF1 MUTATED U2AF1 WILD-TYPE 
             11             458 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              3             168 
$`U2AF1 MUTATED`
TCGA-55-1595 TCGA-49-4505 TCGA-49-6744 TCGA-50-5941 TCGA-50-8460 TCGA-55-7727 
       48.62        14.07        55.33        48.46        27.25         3.91 
TCGA-55-7903 TCGA-78-7145 TCGA-78-8655 TCGA-86-8585 TCGA-MP-A4T4 
       18.64        27.16        77.59        11.61        86.04 

$`U2AF1 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       23.05         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       29.98        12.00        30.02        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       25.02        24.00         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       37.71        49.05        44.61         4.37        46.98        44.42 
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-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       19.46         7.17        36.07        18.87        23.64        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
        8.55        15.98        15.32         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
        8.45        15.12        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
        3.91        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       10.13        36.99        36.79        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       35.21        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       40.73        15.25        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
       70.26        31.30        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7907 TCGA-55-7910 
       22.03        23.15        25.41        15.39        11.28        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       23.08         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       13.74        20.28        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.62        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        3.25         0.92        15.81        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-69-7760 
       18.84        14.04        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41        13.41        13.51        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       19.43         8.42         6.90        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 
        4.31        30.31         9.24         1.25        50.33        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       77.85        43.82        85.15        49.84        36.66       108.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      100.57       163.10         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-78-7167 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-78-8662 TCGA-80-5608 
       39.35        10.55       232.18        39.75       110.50        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 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-86-8668 TCGA-86-8669 
       31.20        23.05        21.47        14.60        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
        1.08        19.00        41.82        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       25.48        18.54         0.59        15.91        18.67         5.39 
TCGA-97-8175 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-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       36.76         1.45        21.57        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       19.00        14.30        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE 
       49.35        37.35        58.85         5.49        41.59        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 
       74.33         0.13         1.64        47.08         0.49         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  U2AF1 MUTATED U2AF1 WILD-TYPE 
           3.91            0.00 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
          86.04          238.29 
  U2AF1 MUTATED U2AF1 WILD-TYPE 
          27.25           21.44 
[1] "3.9 - 86.0 (27.2)"  "0.0 - 238.3 (21.4)"
[1] "hr=" "1.9"
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      117      131        45        64         68
                 vv
clus              STAGE IIIB STAGE IV
  U2AF1 MUTATED            0        1
  U2AF1 WILD-TYPE         11       23
D17V3, multiclass
            clus
vv           U2AF1 MUTATED U2AF1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             117
  STAGE IB               1             131
  STAGE IIA              1              45
  STAGE IIB              2              64
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              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
  U2AF1 MUTATED     5   5   0   1
  U2AF1 WILD-TYPE 151 256  43  17
D17V4, multiclass
    clus
vv   U2AF1 MUTATED U2AF1 WILD-TYPE
  T1             5             151
  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 303  85    70
D17V5, multiclass
       clus
vv      U2AF1 MUTATED U2AF1 WILD-TYPE
  N0                5             303
  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 253 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF1 MUTATED      7    4
  U2AF1 WILD-TYPE  253  217
        clus
vv       U2AF1 MUTATED U2AF1 WILD-TYPE
  FEMALE             7             253
  MALE               4             217
[1] 2 2
[1] FALSE
D17V8, binary
                 cls
clus                0   1
  U2AF1 MUTATED    10   1
  U2AF1 WILD-TYPE 374  54
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF1 MUTATED     10    1
  U2AF1 WILD-TYPE  374   54
     clus
vv    U2AF1 MUTATED U2AF1 WILD-TYPE
  NO             10             374
  YES             1              54
[1] 2 2
[1] FALSE
D17V9, continuous
[1] "Remove cluster labels:" "U2AF1 MUTATED"         
clus
  U2AF1 MUTATED U2AF1 WILD-TYPE 
              2             120 
     TCGA-44-6147      TCGA-44-A47F      TCGA-49-6742      TCGA-55-7573 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7914      TCGA-55-8205      TCGA-55-8511 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8621      TCGA-55-A491      TCGA-55-A492 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-64-1677      TCGA-73-4662      TCGA-73-7498      TCGA-93-8067 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-35-4122      TCGA-35-4123      TCGA-35-5375 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-44-3396      TCGA-44-3918      TCGA-44-4112      TCGA-44-6144 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-7660      TCGA-49-4486      TCGA-49-4494 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-49-4506      TCGA-49-4510      TCGA-49-6743      TCGA-53-7624 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-53-A4EZ      TCGA-55-5899      TCGA-55-7283      TCGA-55-7574 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-55-7910      TCGA-55-7913      TCGA-55-7995      TCGA-55-8089 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-55-8096      TCGA-55-8208      TCGA-55-8507      TCGA-55-8508 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8513      TCGA-55-8620      TCGA-55-A48Z 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1681      TCGA-64-5775 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      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-73-7499 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-6562      TCGA-86-6851 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-86-7701      TCGA-86-7711      TCGA-86-7713      TCGA-86-7714 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-86-7953      TCGA-86-7954      TCGA-86-7955      TCGA-86-8054 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8073      TCGA-86-8074 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-86-8075      TCGA-86-8076      TCGA-86-8278      TCGA-86-8279 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-86-8280      TCGA-86-8281      TCGA-86-8358      TCGA-86-8359 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-A456 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6829      TCGA-91-6849 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-93-7347      TCGA-93-7348      TCGA-93-A4JN      TCGA-93-A4JO 
"U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" "U2AF1 WILD-TYPE" 
     TCGA-95-7567      TCGA-99-7458      TCGA-MN-A4N4      TCGA-MN-A4N5 
"U2AF1 WILD-TYPE" "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                         17                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  U2AF1 MUTATED                                                    6
  U2AF1 WILD-TYPE                                                290
                 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                                      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                                   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 304  11   4  25
D17V13, multiclass
    clus
vv   U2AF1 MUTATED U2AF1 WILD-TYPE
  R0             8             304
  R1             1              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
  U2AF1 MUTATED                                  0     1
  U2AF1 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  U2AF1 MUTATED                           0     9
  U2AF1 WILD-TYPE                        30   369
D17V14, multiclass
                                  clus
vv                                 U2AF1 MUTATED U2AF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    0              30
  WHITE                                        9             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"
D17V15, binary
                 cls
clus                0   1
  U2AF1 MUTATED     0   6
  U2AF1 WILD-TYPE   6 345
[1] "tbl2"
                 cls
clus              [,1] [,2]
  U2AF1 MUTATED      0    6
  U2AF1 WILD-TYPE    6  345
                        clus
vv                       U2AF1 MUTATED U2AF1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             345
[1] 2 2
[1] FALSE

Clustering(18) Variable = ERBB2 MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2               0   1
  ERBB2 MUTATED     7   4
  ERBB2 WILD-TYPE 291 167
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             11             458 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              4             167 
$`ERBB2 MUTATED`
TCGA-05-4384 TCGA-05-4434 TCGA-38-4629 TCGA-05-5715 TCGA-44-2656 TCGA-44-3396 
       14.01        15.02        28.41         2.04        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-05-4382 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96         9.96         8.02        20.05         9.01        26.01 
TCGA-05-5420 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 
       15.02        35.28        11.64        14.73        26.30        38.10 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 
       23.93        27.78        86.01        18.31        29.00        29.23 
TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 
        9.37        11.08        46.72        16.04        17.16        11.64 
TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 
       40.60        21.47        41.69        23.05        48.62         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.79         7.99        16.01        23.18        14.53        21.44 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 
        6.15        19.66        19.73        17.98        16.93        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 
       32.12        18.15        13.68        16.93        22.65        20.58 
TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       19.59        20.19        20.65        13.87        52.60        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 
       39.09         8.48        50.24        10.55        85.32        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       16.18         1.45         6.12        17.29        16.54         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       15.68        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       10.09        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       47.05        19.00         2.99        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-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-38-4632 
        8.68        97.74       120.79        37.71        49.05        44.61 
TCGA-38-A44F TCGA-44-2657 TCGA-44-2665 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 
        4.37        44.42        42.77        38.24        34.06        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       19.46         7.17        36.07        18.87        23.64        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
        8.55        15.98        15.32        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       55.33        22.26        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       53.16        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 
       34.29        30.54        13.94        35.21        30.58        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       80.52         5.62        42.51        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       53.65         3.88        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26        31.30        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       20.02        27.09        32.71        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       25.41        15.39        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.44        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42        17.56        15.72        14.47         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       14.66         1.58        12.33        20.71        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       29.92        56.81        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-69-7760 TCGA-69-7761 
       14.04        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
       13.41        13.51        14.01        13.45         4.24        19.43 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        8.42         6.90        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       30.31         9.24         1.25        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       93.11        27.09         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        11.61        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-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
        1.08        19.00        41.82        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       15.39        16.41        14.30        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       19.76        20.84        18.67        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        1.45        21.57        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       14.30        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE 
       37.35        86.04        58.85         5.49        41.59        29.46 
TCGA-MP-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 
       74.33         0.13         1.64        47.08         0.49         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           21.47 
[1] "2.0 - 47.0 (18.7)"  "0.0 - 238.3 (21.5)"
[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      119      129        45        64         68
                 vv
clus              STAGE IIIB STAGE IV
  ERBB2 MUTATED            0        1
  ERBB2 WILD-TYPE         11       23
D18V3, multiclass
            clus
vv           ERBB2 MUTATED ERBB2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             119
  STAGE IB               3             129
  STAGE IIA              1              45
  STAGE IIB              2              64
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              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
  ERBB2 MUTATED     2   7   1   1
  ERBB2 WILD-TYPE 154 254  42  17
D18V4, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  T1             2             154
  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 302  86    70
D18V5, multiclass
       clus
vv      ERBB2 MUTATED ERBB2 WILD-TYPE
  N0                6             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"
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 255 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      5    6
  ERBB2 WILD-TYPE  255  215
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  FEMALE             5             255
  MALE               6             215
[1] 2 2
[1] FALSE
D18V8, binary
                 cls
clus                0   1
  ERBB2 MUTATED     8   1
  ERBB2 WILD-TYPE 376  54
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      8    1
  ERBB2 WILD-TYPE  376   54
     clus
vv    ERBB2 MUTATED ERBB2 WILD-TYPE
  NO              8             376
  YES             1              54
[1] 2 2
[1] FALSE
D18V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ERBB2 MUTATED                            0                                 4
  ERBB2 WILD-TYPE                         17                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ERBB2 MUTATED                                                    6
  ERBB2 WILD-TYPE                                                290
                 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                                      17
  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                                   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 305  12   3  24
D18V13, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  R0             7             305
  R1             0              12
  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                        30   371
D18V14, multiclass
                                  clus
vv                                 ERBB2 MUTATED ERBB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    0              30
  WHITE                                        7             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"
D18V15, binary
                 cls
clus                0   1
  ERBB2 MUTATED     0   8
  ERBB2 WILD-TYPE   6 343
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      0    8
  ERBB2 WILD-TYPE    6  343
                        clus
vv                       ERBB2 MUTATED ERBB2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             8             343
[1] 2 2
[1] FALSE

Clustering(19) Variable = CDKN2A MUTATION ANALYSIS
D19V1, survival
                  sevent
clus2                0   1
  CDKN2A MUTATED    12   4
  CDKN2A WILD-TYPE 286 167
  CDKN2A MUTATED CDKN2A WILD-TYPE 
              16              453 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               4              167 
$`CDKN2A MUTATED`
TCGA-55-8205 TCGA-55-A492 TCGA-93-8067 TCGA-05-4426 TCGA-05-4433 TCGA-38-4625 
       19.69        19.59         6.12        26.01        24.00        97.74 
TCGA-44-5645 TCGA-44-7662 TCGA-49-4505 TCGA-50-6595 TCGA-53-A4EZ TCGA-55-8089 
       28.01         7.17        14.07         6.21        35.21        23.08 
TCGA-67-3771 TCGA-78-7148 TCGA-86-8585 TCGA-97-8547 
       20.05        20.58        11.61        21.60 

$`CDKN2A WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       17.98        16.93        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       22.65        20.58        20.19        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       13.71        16.18         1.45        17.29        16.54         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       15.68        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       10.09        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       47.05        19.00         2.99        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 TCGA-05-5425 
       30.02        21.99        25.02        25.02         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-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 
      120.79        37.71        49.05        44.61         4.37        46.98 
TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       44.42        42.77        37.15        38.24        34.06        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 
       26.56        33.30        28.37        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
       19.46        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4506 
       76.21        28.11        28.57        12.66        35.54        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        48.46        60.72        57.53        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6673 
       42.35         3.91        25.55        11.05        12.16         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99        36.79        27.25        34.29        30.54 
TCGA-53-7813 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       13.94        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       40.73        15.25        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
       70.26        31.30        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
       22.03         3.91        23.15        25.41        15.39        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 
       11.28        34.19        17.65        18.44        19.82        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       29.72        15.19         5.06        17.79        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       29.19        22.16        15.42        17.56        15.72        14.47 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36        13.74        20.28        17.72        19.96        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
       17.10        17.62        14.66         1.58        12.33        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 
       21.40         3.25         0.92        15.81        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-64-1679 TCGA-64-1681 
       39.25        40.96        29.92        56.81        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-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       18.84        14.04        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41        13.41        13.51        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       19.43         8.42         6.90        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 
        4.31        30.31         9.24         1.25        50.33        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       77.85        43.82        85.15        49.84        36.66       108.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 
      100.57       163.10        27.16         5.69        19.27       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 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-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        12.23        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
       23.61         1.08        19.00        41.82        18.67        12.39 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       27.29         2.76        19.89        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       61.48        25.48        18.54         0.59        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 
        5.39        18.12        15.39        16.41        14.30        20.58 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       36.76         1.45        21.57        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       19.00        14.30        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       49.35        37.35        86.04        58.85         5.49        41.59 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        24.36        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        74.33         0.13         1.64        47.08         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            6.12             0.00 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           97.74           238.29 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
          20.315           21.470 
[1] "6.1 - 97.7 (20.3)"  "0.0 - 238.3 (21.5)"
[1] "hr=" "1.1"
D19V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CDKN2A MUTATED         0        4        6         2         2          2
  CDKN2A WILD-TYPE       4      117      126        44        64         68
                  vv
clus               STAGE IIIB STAGE IV
  CDKN2A MUTATED            0        0
  CDKN2A WILD-TYPE         11       24
D19V3, multiclass
            clus
vv           CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE I                 0                4
  STAGE IA                4              117
  STAGE IB                6              126
  STAGE IIA               2               44
  STAGE IIB               2               64
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                0               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
  CDKN2A MUTATED     4  12   0   0
  CDKN2A WILD-TYPE 152 249  43  18
D19V4, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  T1              4              152
  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 298  86    70
D19V5, multiclass
       clus
vv      CDKN2A MUTATED CDKN2A WILD-TYPE
  N0                10              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"
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 252 213
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      8    8
  CDKN2A WILD-TYPE  252  213
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE              8              252
  MALE                8              213
[1] 2 2
[1] FALSE
D19V8, binary
                  cls
clus                 0   1
  CDKN2A MUTATED    11   2
  CDKN2A WILD-TYPE 373  53
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED     11    2
  CDKN2A WILD-TYPE  373   53
     clus
vv    CDKN2A MUTATED CDKN2A WILD-TYPE
  NO              11              373
  YES              2               53
[1] 2 2
[1] FALSE
D19V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CDKN2A MUTATED                            1                                 4
  CDKN2A WILD-TYPE                         16                                98
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CDKN2A MUTATED                                                   10
  CDKN2A WILD-TYPE                                                286
                  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                                       16
  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                     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 302  12   4  23
D19V13, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  R0             10              302
  R1              0               12
  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                        28   368
D19V14, multiclass
                                  clus
vv                                 CDKN2A MUTATED CDKN2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     2               28
  WHITE                                        10              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"
D19V15, binary
                  cls
clus                 0   1
  CDKN2A MUTATED     1  11
  CDKN2A WILD-TYPE   5 340
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      1   11
  CDKN2A WILD-TYPE    5  340
                        clus
vv                       CDKN2A MUTATED CDKN2A WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             11              340
[1] 2 2
[1] FALSE

Clustering(20) Variable = SRPX MUTATION ANALYSIS
D20V1, survival
                sevent
clus2              0   1
  SRPX MUTATED     9   5
  SRPX WILD-TYPE 289 166
  SRPX MUTATED SRPX WILD-TYPE 
            14            455 
  SRPX MUTATED SRPX WILD-TYPE 
             5            166 
$`SRPX MUTATED`
TCGA-95-7043 TCGA-97-A4LX TCGA-05-4390 TCGA-05-4432 TCGA-38-4628 TCGA-44-2665 
       16.54        20.19        37.02        25.02        49.05        42.77 
TCGA-44-3396 TCGA-44-7659 TCGA-49-4514 TCGA-50-6593 TCGA-78-7155 TCGA-93-7348 
       37.15        22.72        55.89        11.05        38.50        17.46 
TCGA-97-7938 TCGA-97-A4M6 
        0.59        18.67 

$`SRPX WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       17.29         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       17.92        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        10.09        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4395 TCGA-05-4397 
       10.09        50.07         3.98        45.01         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       47.05        19.00         2.99        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 
       30.02        21.99        26.01        25.02        24.00         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-38-4632 TCGA-38-A44F 
        8.68        97.74       120.79        37.71        44.61         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       46.98        44.42        38.24        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 
       21.63        23.18        32.45        61.28        16.44        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 TCGA-49-6744 
       32.84         8.81        29.46        29.75        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        48.46        60.72        57.53        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
       42.35         3.91        25.55        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99        36.79        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        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
      107.21        70.26        31.30        28.67        20.02        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
       32.71        22.03         3.91        23.15        25.41        15.39 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       18.64        11.28        34.19        17.65        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       29.23        29.72        15.19        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.72        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       19.96        26.01        17.10        17.62        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       12.33        20.71        21.40         3.25         0.92        15.81 
TCGA-55-A4DG TCGA-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-64-1679 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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        19.43         8.42         6.90 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       23.38        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
        1.25        50.33        66.64        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       49.84        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
      119.51        19.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        9.57       104.19       238.29        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59       110.50        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        1.18        19.82        22.45        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       41.82        18.67        12.39        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       42.25        64.60        63.52        61.48        25.48        18.54 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       15.91        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       14.30        21.60        20.58        21.44        19.76        20.84 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
       24.56        34.85        36.76         1.45        21.57        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 
       35.47        32.48        19.00        14.30        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        5.49        41.59        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       47.08         0.49         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          21.44 
[1] "0.6 - 55.9 (23.9)"  "0.0 - 238.3 (21.4)"
[1] "hr=" "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      115      129        46        63         68
                vv
clus             STAGE IIIB STAGE IV
  SRPX MUTATED            0        0
  SRPX WILD-TYPE         11       24
D20V3, multiclass
            clus
vv           SRPX MUTATED SRPX WILD-TYPE
  STAGE I               0              4
  STAGE IA              6            115
  STAGE IB              3            129
  STAGE IIA             0             46
  STAGE IIB             3             63
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              0             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
  SRPX MUTATED     7   7   0   0
  SRPX WILD-TYPE 149 254  43  18
D20V4, multiclass
    clus
vv   SRPX MUTATED SRPX WILD-TYPE
  T1            7            149
  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 299  86    70
D20V5, multiclass
       clus
vv      SRPX MUTATED SRPX WILD-TYPE
  N0               9            299
  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 250 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED     10    4
  SRPX WILD-TYPE  250  217
        clus
vv       SRPX MUTATED SRPX WILD-TYPE
  FEMALE           10            250
  MALE              4            217
[1] 2 2
[1] FALSE
D20V8, binary
                cls
clus               0   1
  SRPX MUTATED    12   1
  SRPX WILD-TYPE 372  54
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED     12    1
  SRPX WILD-TYPE  372   54
     clus
vv    SRPX MUTATED SRPX WILD-TYPE
  NO            12            372
  YES            1             54
[1] 2 2
[1] FALSE
D20V9, continuous
[1] "Remove cluster labels:" "SRPX MUTATED"          
clus
  SRPX MUTATED SRPX WILD-TYPE 
             2            120 
    TCGA-44-6147     TCGA-44-A47F     TCGA-49-6742     TCGA-55-7573 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-55-7725     TCGA-55-7914     TCGA-55-8205     TCGA-55-8511 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8621     TCGA-55-A491     TCGA-55-A492 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-64-1677     TCGA-73-4662     TCGA-73-7498     TCGA-93-8067 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-35-4122     TCGA-35-4123     TCGA-35-5375 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-44-3918     TCGA-44-4112     TCGA-44-6144     TCGA-44-6775 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-44-7660     TCGA-49-4486     TCGA-49-4494     TCGA-49-4505 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-49-4506     TCGA-49-4510     TCGA-49-6743     TCGA-49-6744 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-53-7624     TCGA-53-A4EZ     TCGA-55-5899     TCGA-55-7283 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-55-7574     TCGA-55-7910     TCGA-55-7913     TCGA-55-7995 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-55-8089     TCGA-55-8096     TCGA-55-8208     TCGA-55-8507 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-55-8508     TCGA-55-8512     TCGA-55-8513     TCGA-55-8620 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A494     TCGA-62-8394 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-62-8395     TCGA-62-8397     TCGA-62-8398     TCGA-62-8399 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-62-8402     TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-62-A46S     TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-62-A470     TCGA-62-A471     TCGA-62-A472     TCGA-64-1681 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-64-5775     TCGA-64-5778     TCGA-69-7974     TCGA-69-8254 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-71-6725     TCGA-71-8520     TCGA-73-4659     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-73-7499     TCGA-75-5122     TCGA-83-5908     TCGA-86-6562 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-86-6851     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7953     TCGA-86-7954     TCGA-86-7955 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-86-8054     TCGA-86-8055     TCGA-86-8056     TCGA-86-8073 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-86-8074     TCGA-86-8075     TCGA-86-8076     TCGA-86-8278 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-86-8279     TCGA-86-8280     TCGA-86-8281     TCGA-86-8358 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6829 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-91-6849     TCGA-93-7347     TCGA-93-A4JN     TCGA-93-A4JO 
"SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" "SRPX WILD-TYPE" 
    TCGA-95-7567     TCGA-99-7458     TCGA-MN-A4N4     TCGA-MN-A4N5 
"SRPX WILD-TYPE" "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                         17                                96
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SRPX MUTATED                                                    6
  SRPX WILD-TYPE                                                290
                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                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              96
  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"
D20V11, continuous
D20V12, continuous
                vv
clus              R0  R1  R2  RX
  SRPX MUTATED    10   0   0   0
  SRPX WILD-TYPE 302  12   4  25
D20V13, multiclass
    clus
vv   SRPX MUTATED SRPX WILD-TYPE
  R0           10            302
  R1            0             12
  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                        30   366
D20V14, multiclass
                                  clus
vv                                 SRPX MUTATED SRPX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             30
  WHITE                                      12            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"
D20V15, binary
                cls
clus               0   1
  SRPX MUTATED     0  10
  SRPX WILD-TYPE   6 341
[1] "tbl2"
                cls
clus             [,1] [,2]
  SRPX MUTATED      0   10
  SRPX WILD-TYPE    6  341
                        clus
vv                       SRPX MUTATED SRPX WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           10            341
[1] 2 2
[1] FALSE

Clustering(21) Variable = ATM MUTATION ANALYSIS
D21V1, survival
               sevent
clus2             0   1
  ATM MUTATED    26  14
  ATM WILD-TYPE 272 157
  ATM MUTATED ATM WILD-TYPE 
           40           429 
  ATM MUTATED ATM WILD-TYPE 
           14           157 
$`ATM MUTATED`
TCGA-05-4382 TCGA-55-1595 TCGA-97-A4M3 TCGA-L9-A443 TCGA-05-4390 TCGA-05-4417 
       19.96        48.62        17.75         6.35        37.02        14.96 
TCGA-49-4486 TCGA-49-4507 TCGA-49-4510 TCGA-53-7624 TCGA-53-7813 TCGA-55-6642 
       76.21         8.81        29.46        34.29        13.94        80.52 
TCGA-55-6971 TCGA-55-7815 TCGA-55-8508 TCGA-62-8398 TCGA-62-A46Y TCGA-64-1681 
       46.03        25.41        20.28        14.60        13.61        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-67-6215 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 
       87.98         2.04         5.72         7.56         4.41        13.41 
TCGA-69-8253 TCGA-69-8255 TCGA-73-4659 TCGA-78-7156 TCGA-78-7159 TCGA-78-7539 
       14.01         4.24        23.38        32.09        64.90        26.01 
TCGA-80-5608 TCGA-86-8054 TCGA-86-A4JF TCGA-93-A4JN TCGA-95-7567 TCGA-95-A4VP 
       93.11        37.74        24.23        23.61        18.67        19.89 
TCGA-97-8176 TCGA-MN-A4N4 TCGA-MP-A4TI TCGA-NJ-A4YP 
       15.39        38.63        14.10         1.64 

$`ATM WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       14.01         9.96         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        5.79         7.79         7.99        16.01        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       21.44         6.15        19.66        19.73        17.98        16.93 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       19.69        32.12        18.15        13.68        16.93        22.65 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       20.58        19.59        20.19        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       13.71        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A444 
       20.19        20.52        20.68        24.30        23.80        10.09 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 
       27.19         5.29        31.23         2.43        10.09        50.07 
TCGA-05-4250 TCGA-05-4389 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
        3.98        45.01         0.00        24.03        47.05        19.00 
TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        2.99        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        24.00         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 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-38-4632 TCGA-38-A44F TCGA-44-2656 
      120.79        37.71        49.05        44.61         4.37        46.98 
TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        23.18        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       22.72        19.46         7.17        36.07        18.87        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       12.66         8.55        15.98        15.32         9.44        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-49-4505 TCGA-49-4506 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
       14.07        32.84        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        48.46        60.72        57.53        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 
        0.72        10.13        36.99        36.79        27.25        30.54 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       35.21        30.58        14.30         5.62        42.51        40.73 
TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       15.25        53.65         3.88        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       92.81        24.99        40.54       107.21        70.26        31.30 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
       28.67        20.02        27.09        32.71        22.03         3.91 
TCGA-55-7728 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       23.15        15.39        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.44        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42        17.56        15.72        14.47         0.36        13.74 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
        1.58        12.33        20.71        21.40         3.25         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
       15.81        19.99         4.57        39.98        42.38        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       49.25        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 
       72.30        39.25        40.96        29.92        56.81        81.80 
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-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
       14.04        14.73         4.64         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7980 TCGA-69-8254 TCGA-69-A59K 
       13.61         5.42         6.05        13.51        13.45        19.43 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        8.42         6.90        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
        9.24         1.25        50.33        66.64        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       85.15        49.84        36.66       108.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7160 
       39.95       119.51        19.50        38.50         5.88        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        9.57       104.19       238.29        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
        8.02        53.33        39.35        10.55       232.18        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       77.59       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        11.61 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       29.46        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        12.23        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
        1.08        19.00        41.82        12.39        27.29         2.76 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       42.25        64.60        63.52        61.48        25.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
        0.59        15.91        18.67         5.39        18.12        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       14.30        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N5 
       18.08        35.47        32.48        19.00        14.30         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
        5.49        41.59        29.46        11.05        24.36        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        71.05        74.33         0.13        47.08         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  ATM MUTATED ATM WILD-TYPE 
         1.64          0.00 
  ATM MUTATED ATM WILD-TYPE 
        93.11        238.29 
  ATM MUTATED ATM WILD-TYPE 
        20.12         21.47 
[1] "1.6 - 93.1 (20.1)"  "0.0 - 238.3 (21.5)"
[1] "hr=" "1"  
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      112      121        42        60         63
               vv
clus            STAGE IIIB STAGE IV
  ATM MUTATED            1        4
  ATM WILD-TYPE         10       20
D21V3, multiclass
            clus
vv           ATM MUTATED ATM WILD-TYPE
  STAGE I              0             4
  STAGE IA             9           112
  STAGE IB            11           121
  STAGE IIA            4            42
  STAGE IIB            6            60
  STAGE IIIA           7            63
  STAGE IIIB           1            10
  STAGE IV             4            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
  ATM MUTATED    10  26   3   3
  ATM WILD-TYPE 146 235  40  15
D21V4, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  T1          10           146
  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 283  78    67
D21V5, multiclass
       clus
vv      ATM MUTATED ATM WILD-TYPE
  N0             25           283
  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 238 201
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     22   20
  ATM WILD-TYPE  238  201
        clus
vv       ATM MUTATED ATM WILD-TYPE
  FEMALE          22           238
  MALE            20           201
[1] 2 2
[1] FALSE
D21V8, binary
               cls
clus              0   1
  ATM MUTATED    35   5
  ATM WILD-TYPE 349  50
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     35    5
  ATM WILD-TYPE  349   50
     clus
vv    ATM MUTATED ATM WILD-TYPE
  NO           35           349
  YES           5            50
[1] 2 2
[1] FALSE
D21V9, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ATM MUTATED                            5                                13
  ATM WILD-TYPE                         12                                89
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ATM MUTATED                                                   19
  ATM WILD-TYPE                                                277
               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            12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                           13            89
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          19           277
  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 283  12   4  23
D21V13, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  R0          29           283
  R1           0            12
  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                        27   347
D21V14, multiclass
                                  clus
vv                                 ATM MUTATED ATM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             6
  BLACK OR AFRICAN AMERICAN                  3            27
  WHITE                                     31           347
[1] 4 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   4 324
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      2   27
  ATM WILD-TYPE    4  324
                        clus
vv                       ATM MUTATED ATM WILD-TYPE
  HISPANIC OR LATINO               2             4
  NOT HISPANIC OR LATINO          27           324
[1] 2 2
[1] FALSE

Clustering(22) Variable = TCEAL5 MUTATION ANALYSIS
D22V1, survival
                  sevent
clus2                0   1
  TCEAL5 MUTATED     9   4
  TCEAL5 WILD-TYPE 289 167
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
              13              456 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
               4              167 
$`TCEAL5 MUTATED`
TCGA-44-6776 TCGA-73-4662 TCGA-44-5644 TCGA-44-6144 TCGA-49-6767 TCGA-50-8457 
       86.01        82.68        28.37        23.77        22.26        36.99 
TCGA-53-A4EZ TCGA-55-7574 TCGA-55-8507 TCGA-75-5125 TCGA-75-6214 TCGA-86-8073 
       35.21        32.71        13.74        66.64        36.66        24.33 
TCGA-MP-A4T4 
       86.04 

$`TCEAL5 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-7661 
       14.73        26.30        38.10        23.93        27.78        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       52.60        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       13.71        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        10.09        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         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-44-5645 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       28.01        19.56        23.15        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
       61.28        16.44        22.72        19.46         7.17        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       18.87        23.64        12.66         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
        9.44        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-50-5044 
       29.46        29.75        55.89        53.29        55.33        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47       101.72        15.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
        8.22         9.27        14.27        78.67         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       48.46        60.72        57.53        53.16        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05        12.16         6.21         0.72        10.13 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-5899 
       36.79        27.25        34.29        30.54        13.94        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       14.30        80.52         5.62        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       46.03        53.65         3.88        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       92.81        24.99        40.54       107.21        70.26        31.30 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       28.67        20.02        27.09        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       25.41        15.39        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.44        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
       15.42        17.56        15.72        14.47         0.36        20.28 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
        1.58        12.33        20.71        21.40         3.25         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       56.81        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-69-7760 TCGA-69-7761 TCGA-69-7763 
       14.73         5.72         4.64         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        13.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       13.51        14.01        13.45         4.24        19.43         8.42 
TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        6.90        23.38        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
        9.24         1.25        50.33        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       49.84       108.66       100.57       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        9.57       104.19       238.29        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59       110.50        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.89        35.24        37.74         4.08         4.57         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       22.82        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60        11.61        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-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-91-6840 
       10.62        41.36         1.97        10.19         2.60        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45        17.46        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       41.82        18.67        12.39        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       42.25        64.60        63.52        61.48        25.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59        15.91        18.67         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.57        18.08        35.47        32.48        19.00        14.30 
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-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.85         5.49        41.59        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        47.08         0.49         0.43        19.82        59.11 

  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
           13.74             0.00 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
           86.04           238.29 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
          35.210           20.775 
[1] "13.7 - 86.0 (35.2)" "0.0 - 238.3 (20.8)"
[1] "hr=" "1.9"
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      116      129        45        63         69
                  vv
clus               STAGE IIIB STAGE IV
  TCEAL5 MUTATED            0        0
  TCEAL5 WILD-TYPE         11       24
D22V3, multiclass
            clus
vv           TCEAL5 MUTATED TCEAL5 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                5              116
  STAGE IB                3              129
  STAGE IIA               1               45
  STAGE IIB               3               63
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               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
  TCEAL5 MUTATED     5   7   1   0
  TCEAL5 WILD-TYPE 151 254  42  18
D22V4, multiclass
    clus
vv   TCEAL5 MUTATED TCEAL5 WILD-TYPE
  T1              5              151
  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 299  86    71
D22V5, multiclass
       clus
vv      TCEAL5 MUTATED TCEAL5 WILD-TYPE
  N0                 9              299
  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 252 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      8    5
  TCEAL5 WILD-TYPE  252  216
        clus
vv       TCEAL5 MUTATED TCEAL5 WILD-TYPE
  FEMALE              8              252
  MALE                5              216
[1] 2 2
[1] FALSE
D22V8, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED    10   2
  TCEAL5 WILD-TYPE 374  53
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED     10    2
  TCEAL5 WILD-TYPE  374   53
     clus
vv    TCEAL5 MUTATED TCEAL5 WILD-TYPE
  NO              10              374
  YES              2               53
[1] 2 2
[1] FALSE
D22V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TCEAL5 MUTATED                            1                                 1
  TCEAL5 WILD-TYPE                         16                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TCEAL5 MUTATED                                                   10
  TCEAL5 WILD-TYPE                                                286
                  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                                       16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               101
  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"
D22V11, continuous
D22V12, continuous
                  vv
clus                R0  R1  R2  RX
  TCEAL5 MUTATED     7   1   0   2
  TCEAL5 WILD-TYPE 305  11   4  23
D22V13, multiclass
    clus
vv   TCEAL5 MUTATED TCEAL5 WILD-TYPE
  R0              7              305
  R1              1               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
  TCEAL5 MUTATED                                  0     0
  TCEAL5 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TCEAL5 MUTATED                           1    10
  TCEAL5 WILD-TYPE                        29   368
D22V14, multiclass
                                  clus
vv                                 TCEAL5 MUTATED TCEAL5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               29
  WHITE                                        10              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"
D22V15, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED     1   7
  TCEAL5 WILD-TYPE   5 344
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      1    7
  TCEAL5 WILD-TYPE    5  344
                        clus
vv                       TCEAL5 MUTATED TCEAL5 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO              7              344
[1] 2 2
[1] FALSE

Clustering(23) Variable = PPP3CA MUTATION ANALYSIS
D23V1, survival
                  sevent
clus2                0   1
  PPP3CA MUTATED    10   2
  PPP3CA WILD-TYPE 288 169
  PPP3CA MUTATED PPP3CA WILD-TYPE 
              12              457 
  PPP3CA MUTATED PPP3CA WILD-TYPE 
               2              169 
$`PPP3CA MUTATED`
TCGA-J2-8194 TCGA-05-4422 TCGA-44-5643 TCGA-55-8085 TCGA-55-8514 TCGA-73-4676 
       23.80        12.00        33.30        29.72        17.10         9.24 
TCGA-78-8662 TCGA-86-8585 TCGA-91-8496 TCGA-MN-A4N5 TCGA-MP-A5C7 TCGA-NJ-A4YP 
      110.50        11.61        16.60         2.76        73.91         1.64 

$`PPP3CA WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       17.29        16.54         2.86        15.68        15.65        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       18.18        17.92        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       24.30         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       29.98        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         4.37        46.98        44.42        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
       37.15        38.24        34.06        33.73        26.56        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        48.46        60.72        57.53        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99        36.79        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       30.54        13.94        35.21        30.58        14.30        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        5.62        42.51        40.73        15.25        46.03        53.65 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26        31.30        28.67        20.02 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       27.09        32.71        22.03         3.91        23.15        25.41 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 
       15.39        18.64        11.28        34.19        17.65        18.44 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       19.82        29.23        15.19        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.72        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
       19.96        26.01        17.62        14.66         1.58        12.33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
       20.71        21.40         3.25         0.92        15.81        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 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-64-1679 
       13.61        39.25        40.96        29.92        56.81        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41        13.41        13.51        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 
       13.45         4.24        19.43         8.42         6.90        23.38 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7499 
       26.30        15.35         4.31        30.31         1.25        50.33 
TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 
       66.64        77.85        43.82        85.15        49.84        36.66 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
      108.66       100.57       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      104.19       238.29        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
       53.33        26.01        39.35        10.55       232.18        39.75 
TCGA-78-8655 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       77.59        93.11        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 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-91-6840 TCGA-91-6847 TCGA-91-6848 
        1.97        10.19         2.60        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
        1.15        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
       23.61         1.08        19.00        41.82        18.67        12.39 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       27.29         2.76        19.89        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       61.48        25.48        18.54         0.59        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       20.58        21.44        19.76        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE 
       34.85        36.76         1.45        21.57        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW 
       32.48        19.00        14.30        38.63        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       49.35        37.35        86.04        58.85         5.49        41.59 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-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 
       74.33         0.13        47.08         0.49         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  PPP3CA MUTATED PPP3CA WILD-TYPE 
            1.64             0.00 
  PPP3CA MUTATED PPP3CA WILD-TYPE 
          110.50           238.29 
  PPP3CA MUTATED PPP3CA WILD-TYPE 
           16.85            21.47 
[1] "1.6 - 110.5 (16.9)" "0.0 - 238.3 (21.5)"
[1] "hr=" "2.2"
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      119      125        45        65         69
                  vv
clus               STAGE IIIB STAGE IV
  PPP3CA MUTATED            0        0
  PPP3CA WILD-TYPE         11       24
D23V3, multiclass
            clus
vv           PPP3CA MUTATED PPP3CA WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              119
  STAGE IB                7              125
  STAGE IIA               1               45
  STAGE IIB               1               65
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               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
  PPP3CA MUTATED     2   9   1   0
  PPP3CA WILD-TYPE 154 252  42  18
D23V4, multiclass
    clus
vv   PPP3CA MUTATED PPP3CA WILD-TYPE
  T1              2              154
  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 299  88    71
D23V5, multiclass
       clus
vv      PPP3CA MUTATED PPP3CA WILD-TYPE
  N0                 9              299
  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 255 214
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPP3CA MUTATED      5    7
  PPP3CA WILD-TYPE  255  214
        clus
vv       PPP3CA MUTATED PPP3CA WILD-TYPE
  FEMALE              5              255
  MALE                7              214
[1] 2 2
[1] FALSE
D23V8, binary
                  cls
clus                 0   1
  PPP3CA MUTATED     8   3
  PPP3CA WILD-TYPE 376  52
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPP3CA MUTATED      8    3
  PPP3CA WILD-TYPE  376   52
     clus
vv    PPP3CA MUTATED PPP3CA WILD-TYPE
  NO               8              376
  YES              3               52
[1] 2 2
[1] FALSE
D23V9, continuous
[1] "Remove cluster labels:" "PPP3CA MUTATED"        
clus
  PPP3CA MUTATED PPP3CA WILD-TYPE 
               2              120 
      TCGA-44-6147       TCGA-44-A47F       TCGA-49-6742       TCGA-55-7573 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-55-7725       TCGA-55-7914       TCGA-55-8205       TCGA-55-8511 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-55-8619       TCGA-55-8621       TCGA-55-A491       TCGA-55-A492 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-64-1677       TCGA-73-4662       TCGA-73-7498       TCGA-93-8067 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-35-4122       TCGA-35-4123       TCGA-35-5375 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-44-3396       TCGA-44-3918       TCGA-44-4112       TCGA-44-6144 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-44-6775       TCGA-44-7660       TCGA-49-4486       TCGA-49-4494 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-49-4505       TCGA-49-4506       TCGA-49-4510       TCGA-49-6743 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-49-6744       TCGA-53-7624       TCGA-53-A4EZ       TCGA-55-5899 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7574       TCGA-55-7910       TCGA-55-7913 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-55-7995       TCGA-55-8089       TCGA-55-8096       TCGA-55-8208 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-55-8507       TCGA-55-8508       TCGA-55-8512       TCGA-55-8513 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-55-8620       TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A494 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-62-8394       TCGA-62-8395       TCGA-62-8397       TCGA-62-8398 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O       TCGA-62-A46P 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U       TCGA-62-A46V 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471       TCGA-62-A472 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-64-1681       TCGA-64-5775       TCGA-64-5778       TCGA-69-7974 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-69-8254       TCGA-71-6725       TCGA-71-8520       TCGA-73-4659 
"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-73-7499       TCGA-75-5122       TCGA-83-5908       TCGA-86-6562 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-86-6851       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7953       TCGA-86-7954       TCGA-86-7955 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-86-8054       TCGA-86-8055       TCGA-86-8056       TCGA-86-8073 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-86-8074       TCGA-86-8075       TCGA-86-8076       TCGA-86-8278 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-86-8279       TCGA-86-8280       TCGA-86-8281       TCGA-86-8358 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-86-A456       TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6829 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-91-6849       TCGA-93-7347       TCGA-93-7348       TCGA-93-A4JN 
"PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" "PPP3CA WILD-TYPE" 
      TCGA-93-A4JO       TCGA-95-7567       TCGA-99-7458       TCGA-MN-A4N4 
"PPP3CA WILD-TYPE" "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                         17                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PPP3CA MUTATED                                                    6
  PPP3CA WILD-TYPE                                                290
                  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                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               100
  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                                    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 304  12   4  25
D23V13, multiclass
    clus
vv   PPP3CA MUTATED PPP3CA WILD-TYPE
  R0              8              304
  R1              0               12
  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                        28   370
D23V14, multiclass
                                  clus
vv                                 PPP3CA MUTATED PPP3CA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     2               28
  WHITE                                         8              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"
D23V15, binary
                  cls
clus                 0   1
  PPP3CA MUTATED     0  10
  PPP3CA WILD-TYPE   6 341
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PPP3CA MUTATED      0   10
  PPP3CA WILD-TYPE    6  341
                        clus
vv                       PPP3CA MUTATED PPP3CA WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             10              341
[1] 2 2
[1] FALSE

Clustering(24) Variable = FCRLA MUTATION ANALYSIS
D24V1, survival
                 sevent
clus2               0   1
  FCRLA MUTATED     9   5
  FCRLA WILD-TYPE 289 166
  FCRLA MUTATED FCRLA WILD-TYPE 
             14             455 
  FCRLA MUTATED FCRLA WILD-TYPE 
              5             166 
$`FCRLA MUTATED`
TCGA-91-A4BC TCGA-95-A4VN TCGA-44-2656 TCGA-44-A479 TCGA-50-5933 TCGA-50-6593 
        1.45        18.18        46.98        15.98        78.67        11.05 
TCGA-50-6594 TCGA-55-6970 TCGA-55-7576 TCGA-55-8089 TCGA-69-7973 TCGA-91-8499 
       12.16        15.25        22.03        23.08         7.56         1.18 
TCGA-99-7458 TCGA-MN-A4N5 
       24.56         2.76 

$`FCRLA WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-93-8067 TCGA-93-A4JQ 
       10.55        85.32        13.71        16.18         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 
       16.54         2.86        15.68        15.65        21.40        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        10.09        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 
       49.05        44.61         4.37        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-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47A 
       36.07        18.87        23.64        12.66         8.55        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
        9.44        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 
       29.46        29.75        55.89        53.29        55.33        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 
       49.28         8.22         9.27        14.27         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       48.46        60.72        57.53        53.16        42.35         3.91 
TCGA-50-6592 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       25.55         6.21         0.72        10.13        36.99        36.79 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 
       27.25        34.29        30.54        13.94        35.21        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 
       14.30        80.52         5.62        42.51        40.73        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       53.65         3.88        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26        31.30        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       20.02        27.09        32.71         3.91        23.15        25.41 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 
       15.39        18.64        11.28        34.19        17.65        18.44 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8094 
       19.82        29.23        29.72        15.19         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.72        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       19.96        26.01        17.10        17.62        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       12.33        20.71        21.40         3.25         0.92        15.81 
TCGA-55-A4DG TCGA-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-64-1679 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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        5.42         6.05         4.41        13.41        13.51        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 
       13.45         4.24        19.43         8.42         6.90        23.38 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
       50.33        66.64        77.85        43.82        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       36.66       108.66       100.57       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        9.57       104.19       238.29        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59       110.50        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.60        14.27 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45        17.46        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       41.82        18.67        12.39        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       42.25        64.60        63.52        61.48        25.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59        15.91        18.67         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.84        18.67        34.85        36.76         1.45        21.57 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 
       18.08        35.47        32.48        19.00        14.30        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-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        5.49        41.59        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       47.08         0.49         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 
         15.615          21.570 
[1] "1.2 - 78.7 (15.6)"  "0.0 - 238.3 (21.6)"
[1] "hr=" "1.5"
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      118      127        44        66         66
                 vv
clus              STAGE IIIB STAGE IV
  FCRLA MUTATED            1        0
  FCRLA WILD-TYPE         10       24
D24V3, multiclass
            clus
vv           FCRLA MUTATED FCRLA WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             118
  STAGE IB               5             127
  STAGE IIA              2              44
  STAGE IIB              0              66
  STAGE IIIA             4              66
  STAGE IIIB             1              10
  STAGE IV               0              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
  FCRLA MUTATED     4   8   1   2
  FCRLA WILD-TYPE 152 253  42  16
D24V4, multiclass
    clus
vv   FCRLA MUTATED FCRLA WILD-TYPE
  T1             4             152
  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 298  88    68
D24V5, multiclass
       clus
vv      FCRLA MUTATED FCRLA WILD-TYPE
  N0               10             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"
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 252 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRLA MUTATED      8    7
  FCRLA WILD-TYPE  252  214
        clus
vv       FCRLA MUTATED FCRLA WILD-TYPE
  FEMALE             8             252
  MALE               7             214
[1] 2 2
[1] FALSE
D24V8, binary
                 cls
clus                0   1
  FCRLA MUTATED    10   3
  FCRLA WILD-TYPE 374  52
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRLA MUTATED     10    3
  FCRLA WILD-TYPE  374   52
     clus
vv    FCRLA MUTATED FCRLA WILD-TYPE
  NO             10             374
  YES             3              52
[1] 2 2
[1] FALSE
D24V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FCRLA MUTATED                            0                                 3
  FCRLA WILD-TYPE                         17                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FCRLA MUTATED                                                    9
  FCRLA WILD-TYPE                                                287
                 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                                      17
  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                    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 305  11   4  24
D24V13, multiclass
    clus
vv   FCRLA MUTATED FCRLA WILD-TYPE
  R0             7             305
  R1             1              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
  FCRLA MUTATED                                  0     0
  FCRLA WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FCRLA MUTATED                           3    11
  FCRLA WILD-TYPE                        27   367
D24V14, multiclass
                                  clus
vv                                 FCRLA MUTATED FCRLA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    3              27
  WHITE                                       11             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"
D24V15, binary
                 cls
clus                0   1
  FCRLA MUTATED     0  13
  FCRLA WILD-TYPE   6 338
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRLA MUTATED      0   13
  FCRLA WILD-TYPE    6  338
                        clus
vv                       FCRLA MUTATED FCRLA WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            13             338
[1] 2 2
[1] FALSE

Clustering(25) Variable = ARID2 MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2               0   1
  ARID2 MUTATED    14  10
  ARID2 WILD-TYPE 284 161
  ARID2 MUTATED ARID2 WILD-TYPE 
             24             445 
  ARID2 MUTATED ARID2 WILD-TYPE 
             10             161 
$`ARID2 MUTATED`
TCGA-05-4396 TCGA-38-4631 TCGA-55-7726 TCGA-55-8511 TCGA-67-6217 TCGA-73-4658 
        9.96        11.64        21.44        18.15        13.87        52.60 
TCGA-78-7633 TCGA-93-8067 TCGA-05-4397 TCGA-44-2656 TCGA-44-2657 TCGA-44-8120 
       50.24         6.12        24.03        46.98        44.42         8.55 
TCGA-50-5931 TCGA-50-6592 TCGA-55-7994 TCGA-55-8089 TCGA-62-A46P TCGA-69-7974 
       14.27        25.55        19.82        23.08        19.53         6.05 
TCGA-69-7978 TCGA-73-4675 TCGA-86-6851 TCGA-91-6848 TCGA-91-6849 TCGA-MN-A4N4 
        4.41        30.31         5.88         7.36         1.15        38.63 

$`ARID2 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 
       15.02        15.02        28.41        35.28        14.73        26.30 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       38.10        23.93        27.78        86.01        18.31        29.00 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       29.23         9.37        11.08        46.72        16.04        17.16 
TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 
       11.64        40.60        21.47        41.69        23.05        48.62 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        5.79         7.79         7.99        16.01        23.18        14.53 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 
        6.15        19.66        19.73        17.98        16.93        19.69 
TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 
       32.12        13.68        16.93        22.65        20.58        19.59 
TCGA-55-A4DF TCGA-64-1677 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-8660 
       20.19        20.65        82.68        39.09         8.48        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 
       85.32        13.71        16.18         1.45        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        10.09        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       47.05        19.00         2.99        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        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-38-4632 TCGA-38-A44F TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       44.61         4.37        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       19.56        23.15        21.63        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        22.72        19.46         7.17        36.07        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       23.64        12.66        15.98        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       35.54        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       55.89        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 
      101.72        15.72        60.16        47.41        49.28         8.22 
TCGA-50-5930 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
        9.27        78.67         8.45        15.12        48.46        60.72 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 
       57.53        53.16        42.35         3.91        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 
       34.29        30.54        13.94        35.21        30.58        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       80.52         5.62        42.51        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       53.65         3.88        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26        31.30        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       20.02        27.09        32.71        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       25.41        15.39        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8094 
       18.44        29.23        29.72        15.19         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.72        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       19.96        26.01        17.10        17.62        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       12.33        20.71        21.40         3.25         0.92        15.81 
TCGA-55-A4DG TCGA-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-64-1679 
       13.61        39.25        40.96        29.92        56.81        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        7.56        13.41        13.51        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       19.43         8.42         6.90        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
        4.31         9.24         1.25        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       93.11        27.09        12.36        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 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        11.61        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-8496 TCGA-91-8497 
       10.19         2.60        12.23        27.68        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.18        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
       19.00        41.82        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       15.39        16.41        14.30        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       19.76        20.84        18.67        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        1.45        21.57        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       14.30         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        47.08         0.49         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  ARID2 MUTATED ARID2 WILD-TYPE 
           1.15            0.00 
  ARID2 MUTATED ARID2 WILD-TYPE 
          52.60          238.29 
  ARID2 MUTATED ARID2 WILD-TYPE 
          18.84           21.60 
[1] "1.1 - 52.6 (18.8)"  "0.0 - 238.3 (21.6)"
[1] "hr=" "1.6"
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      118      121        44        63         66
                 vv
clus              STAGE IIIB STAGE IV
  ARID2 MUTATED            1        0
  ARID2 WILD-TYPE         10       24
D25V3, multiclass
            clus
vv           ARID2 MUTATED ARID2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             118
  STAGE IB              11             121
  STAGE IIA              2              44
  STAGE IIB              3              63
  STAGE IIIA             4              66
  STAGE IIIB             1              10
  STAGE IV               0              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
  ARID2 MUTATED     4  17   2   1
  ARID2 WILD-TYPE 152 244  41  17
D25V4, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  T1             4             152
  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 294  83    69
D25V5, multiclass
       clus
vv      ARID2 MUTATED ARID2 WILD-TYPE
  N0               14             294
  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 249 208
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     11   13
  ARID2 WILD-TYPE  249  208
        clus
vv       ARID2 MUTATED ARID2 WILD-TYPE
  FEMALE            11             249
  MALE              13             208
[1] 2 2
[1] FALSE
D25V8, binary
                 cls
clus                0   1
  ARID2 MUTATED    18   2
  ARID2 WILD-TYPE 366  53
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     18    2
  ARID2 WILD-TYPE  366   53
     clus
vv    ARID2 MUTATED ARID2 WILD-TYPE
  NO             18             366
  YES             2              53
[1] 2 2
[1] FALSE
D25V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ARID2 MUTATED                            0                                 7
  ARID2 WILD-TYPE                         17                                95
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ARID2 MUTATED                                                   17
  ARID2 WILD-TYPE                                                279
                 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                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               95
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             279
  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 298  12   4  23
D25V13, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  R0            14             298
  R1             0              12
  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                        28   359
D25V14, multiclass
                                  clus
vv                                 ARID2 MUTATED ARID2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    2              28
  WHITE                                       19             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"
D25V15, binary
                 cls
clus                0   1
  ARID2 MUTATED     0  21
  ARID2 WILD-TYPE   6 330
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      0   21
  ARID2 WILD-TYPE    6  330
                        clus
vv                       ARID2 MUTATED ARID2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            21             330
[1] 2 2
[1] FALSE

Clustering(26) Variable = APC MUTATION ANALYSIS
D26V1, survival
               sevent
clus2             0   1
  APC MUTATED    11   9
  APC WILD-TYPE 287 162
  APC MUTATED APC WILD-TYPE 
           20           449 
  APC MUTATED APC WILD-TYPE 
            9           162 
$`APC MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-38-4631 TCGA-44-7661 TCGA-49-6761 TCGA-05-4397 
       19.96         8.02        11.64        18.31        11.64        24.03 
TCGA-44-A4SS TCGA-49-4507 TCGA-50-5049 TCGA-50-5930 TCGA-50-8457 TCGA-55-5899 
       13.64         8.81       101.72         9.27        36.99        30.58 
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-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 
       14.01         9.96        20.05         9.01        26.01        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 
       15.02        28.41        35.28        14.73        26.30        38.10 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 
       23.93        27.78        86.01        29.00        29.23         9.37 
TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-50-5932 TCGA-50-5935 
       11.08        46.72        16.04        17.16        40.60        21.47 
TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 
       41.69        23.05        48.62         5.79         7.79         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 
       16.01        23.18        14.53        21.44         6.15        19.66 
TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 
       19.73        17.98        16.93        19.69        32.12        18.15 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF 
       13.68        16.93        22.65        20.58        19.59        20.19 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       20.65        13.87        52.60        82.68        39.09         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
       50.24        10.55        85.32        13.71        16.18         1.45 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
        6.12        17.29        16.54         2.86        15.68        15.65 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       21.40        18.18        17.92        20.19        20.52        17.75 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       20.68        24.30        23.80         6.35        10.09        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
        5.29        31.23         2.43        10.09        50.07         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       45.01        37.02         0.00        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        24.00         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 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-38-4632 TCGA-38-A44F TCGA-44-2656 
      120.79        37.71        49.05        44.61         4.37        46.98 
TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        23.18        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       22.72        19.46         7.17        36.07        18.87        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       12.66         8.55        15.98        15.32         9.44        11.54 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       14.07        32.84        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 
       55.33        22.26        20.52        71.47        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       47.41        49.28         8.22        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
        3.91        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       10.13        36.79        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       35.21        14.30        80.52         5.62        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       15.25        46.03        53.65         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       31.30        28.67        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        3.91        23.15        25.41        15.39        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       34.19        17.65        18.44        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       15.19        23.08         5.06        17.79        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       29.19        22.16        15.42        17.56        15.72        14.47 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.36        13.74        20.28        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.62        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 
        3.25         0.92        15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       29.92        56.81        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-69-7760 TCGA-69-7761 
       14.04        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 
       22.68        13.61         5.42         7.56         6.05        13.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       13.51        14.01        13.45         4.24        19.43         8.42 
TCGA-71-8520 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
        6.90        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
        1.25        50.33        66.64        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       49.84        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
        9.57       104.19       238.29        88.14        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
       53.33        26.01        39.35        10.55       232.18        39.75 
TCGA-78-8655 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       77.59        93.11        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 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 
       11.61        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-91-6847 TCGA-91-6848 
       41.36         1.97        10.19         2.60        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 
       17.46        23.61         1.08        19.00        41.82        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       12.39        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       21.60        20.58        21.44        19.76        20.84        18.67 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
       24.56        34.85        36.76         1.45        21.57        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 
       35.47        32.48        19.00        14.30        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        5.49        41.59        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       47.08         0.49         0.43        19.82        59.11 

  APC MUTATED APC WILD-TYPE 
         4.41          0.00 
  APC MUTATED APC WILD-TYPE 
       119.51        238.29 
  APC MUTATED APC WILD-TYPE 
       19.135        21.470 
[1] "4.4 - 119.5 (19.1)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.1"
D26V2, continuous
               vv
clus            STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  APC MUTATED         0        4        6         0         3          5
  APC WILD-TYPE       4      117      126        46        63         65
               vv
clus            STAGE IIIB STAGE IV
  APC MUTATED            0        1
  APC WILD-TYPE         11       23
D26V3, multiclass
            clus
vv           APC MUTATED APC WILD-TYPE
  STAGE I              0             4
  STAGE IA             4           117
  STAGE IB             6           126
  STAGE IIA            0            46
  STAGE IIB            3            63
  STAGE IIIA           5            65
  STAGE IIIB           0            11
  STAGE IV             1            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
  APC MUTATED     5  13   2   0
  APC WILD-TYPE 151 248  41  18
D26V4, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  T1           5           151
  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 297  85    68
D26V5, multiclass
       clus
vv      APC MUTATED APC WILD-TYPE
  N0             11           297
  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 248 213
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     12    8
  APC WILD-TYPE  248  213
        clus
vv       APC MUTATED APC WILD-TYPE
  FEMALE          12           248
  MALE             8           213
[1] 2 2
[1] FALSE
D26V8, binary
               cls
clus              0   1
  APC MUTATED    14   5
  APC WILD-TYPE 370  50
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     14    5
  APC WILD-TYPE  370   50
     clus
vv    APC MUTATED APC WILD-TYPE
  NO           14           370
  YES           5            50
[1] 2 2
[1] FALSE
D26V9, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  APC MUTATED                            0                                 9
  APC WILD-TYPE                         17                                93
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  APC MUTATED                                                   11
  APC WILD-TYPE                                                285
               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            17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            9            93
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          11           285
  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 299  12   3  25
D26V13, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  R0          13           299
  R1           0            12
  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                        29   363
D26V14, multiclass
                                  clus
vv                                 APC MUTATED APC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  1            29
  WHITE                                     15           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"
D26V15, binary
               cls
clus              0   1
  APC MUTATED     0  14
  APC WILD-TYPE   6 337
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED      0   14
  APC WILD-TYPE    6  337
                        clus
vv                       APC MUTATED APC WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO          14           337
[1] 2 2
[1] FALSE

Clustering(27) Variable = ZEB1 MUTATION ANALYSIS
D27V1, survival
                sevent
clus2              0   1
  ZEB1 MUTATED    23   9
  ZEB1 WILD-TYPE 275 162
  ZEB1 MUTATED ZEB1 WILD-TYPE 
            32            437 
  ZEB1 MUTATED ZEB1 WILD-TYPE 
             9            162 
$`ZEB1 MUTATED`
TCGA-44-7671 TCGA-55-1592 TCGA-55-A4DF TCGA-05-4250 TCGA-05-4424 TCGA-35-4123 
       29.23        23.05        20.19         3.98        30.02         5.98 
TCGA-44-2656 TCGA-44-7662 TCGA-49-6743 TCGA-50-5049 TCGA-55-7281 TCGA-55-7283 
       46.98         7.17        53.29       101.72        28.67        20.02 
TCGA-55-8616 TCGA-55-A4DG TCGA-62-A46V TCGA-64-5774 TCGA-64-5779 TCGA-69-7761 
        1.58        19.99        72.30        87.98        28.41         6.12 
TCGA-69-7973 TCGA-69-8254 TCGA-73-4666 TCGA-75-6214 TCGA-78-7146 TCGA-78-7162 
        7.56        13.45        26.30        36.66         5.69       104.19 
TCGA-78-8640 TCGA-86-8585 TCGA-86-A456 TCGA-93-A4JO TCGA-97-7937 TCGA-MN-A4N4 
      232.18        11.61        29.46         1.08        18.54        38.63 
TCGA-MP-A4T2 TCGA-NJ-A4YI 
       37.35         0.13 

$`ZEB1 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       18.31        29.00         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1595 
       17.16        11.64        40.60        21.47        41.69        48.62 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        5.79         7.79         7.99        16.01        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       21.44         6.15        19.66        19.73        17.98        16.93 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       19.69        32.12        18.15        13.68        16.93        22.65 
TCGA-55-A491 TCGA-55-A492 TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       20.58        19.59        20.65        13.87        52.60        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 
       39.09         8.48        50.24        10.55        85.32        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       16.18         1.45         6.12        17.29        16.54         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       15.68        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       10.09        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 
       50.07        45.01        37.02         0.00        24.03        47.05 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
       19.00         2.99        14.96        29.98        12.00        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       26.01        25.02        25.02        24.00         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 
       22.03         9.04         2.04         7.40         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2657 
      120.79        37.71        49.05        44.61         4.37        44.42 
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-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
       19.46        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 
       32.84         8.81        29.46        29.75        55.89        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       22.26        20.52        71.47        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       49.28         8.22         9.27        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
        3.91        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99        36.79        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       13.94        35.21        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
      107.21        70.26        31.30        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        3.91        23.15        25.41        15.39        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       34.19        17.65        18.44        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       15.19        23.08         5.06        17.79        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       29.19        22.16        15.42        17.56        15.72        14.47 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36        13.74        20.28        17.72        19.96        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.10        17.62        14.66        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        3.25         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-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 
       56.81        81.80        38.37         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-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 
        4.64         6.64        22.68        13.61         5.42         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-69-A59K 
        4.41        13.41        13.51        14.01         4.24        19.43 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        8.42         6.90        23.38        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
        9.24         1.25        50.33        66.64        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       85.15        49.84       108.66       100.57       163.10        27.16 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        9.57       238.29        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 
       53.33        26.01        39.35        10.55        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
      110.50        93.11        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-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        12.23        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
       23.61        19.00        41.82        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       25.48         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       15.39        16.41        14.30        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       19.76        20.84        18.67        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        1.45        21.57        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T4 
       14.30         2.76        86.14        58.45        49.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.85         5.49        41.59        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP 
       14.10        19.13        73.91        71.05        74.33         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       47.08         0.49         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 
        24.675         21.440 
[1] "0.1 - 232.2 (24.7)" "0.0 - 238.3 (21.4)"
[1] "hr=" "1.5"
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      110      122        45        65         63
                vv
clus             STAGE IIIB STAGE IV
  ZEB1 MUTATED            0        1
  ZEB1 WILD-TYPE         11       23
D27V3, multiclass
            clus
vv           ZEB1 MUTATED ZEB1 WILD-TYPE
  STAGE I               0              4
  STAGE IA             11            110
  STAGE IB             10            122
  STAGE IIA             1             45
  STAGE IIB             1             65
  STAGE IIIA            7             63
  STAGE IIIB            0             11
  STAGE IV              1             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
  ZEB1 MUTATED    12  17   3   0
  ZEB1 WILD-TYPE 144 244  40  18
D27V4, multiclass
    clus
vv   ZEB1 MUTATED ZEB1 WILD-TYPE
  T1           12            144
  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 285  87    66
D27V5, multiclass
       clus
vv      ZEB1 MUTATED ZEB1 WILD-TYPE
  N0              23            285
  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 248 201
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZEB1 MUTATED     12   20
  ZEB1 WILD-TYPE  248  201
        clus
vv       ZEB1 MUTATED ZEB1 WILD-TYPE
  FEMALE           12            248
  MALE             20            201
[1] 2 2
[1] FALSE
D27V8, binary
                cls
clus               0   1
  ZEB1 MUTATED    25   4
  ZEB1 WILD-TYPE 359  51
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZEB1 MUTATED     25    4
  ZEB1 WILD-TYPE  359   51
     clus
vv    ZEB1 MUTATED ZEB1 WILD-TYPE
  NO            25            359
  YES            4             51
[1] 2 2
[1] FALSE
D27V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ZEB1 MUTATED                            2                                 8
  ZEB1 WILD-TYPE                         15                                94
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ZEB1 MUTATED                                                   16
  ZEB1 WILD-TYPE                                                280
                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                                     15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              94
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            280
  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 294  11   3  24
D27V13, multiclass
    clus
vv   ZEB1 MUTATED ZEB1 WILD-TYPE
  R0           18            294
  R1            1             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
  ZEB1 MUTATED                                  0     1
  ZEB1 WILD-TYPE                                1     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ZEB1 MUTATED                           1    26
  ZEB1 WILD-TYPE                        29   352
D27V14, multiclass
                                  clus
vv                                 ZEB1 MUTATED ZEB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              6
  BLACK OR AFRICAN AMERICAN                   1             29
  WHITE                                      26            352
[1] 4 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   6 328
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZEB1 MUTATED      0   23
  ZEB1 WILD-TYPE    6  328
                        clus
vv                       ZEB1 MUTATED ZEB1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           23            328
[1] 2 2
[1] FALSE

Clustering(28) Variable = SIP1 MUTATION ANALYSIS
D28V1, survival
                sevent
clus2              0   1
  SIP1 MUTATED     2   2
  SIP1 WILD-TYPE 296 169
  SIP1 MUTATED SIP1 WILD-TYPE 
             4            465 
  SIP1 MUTATED SIP1 WILD-TYPE 
             2            169 
$`SIP1 MUTATED`
TCGA-55-1592 TCGA-55-1595 TCGA-44-3919 TCGA-95-7567 
       23.05        48.62        33.73        18.67 

$`SIP1 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        5.79         7.79         7.99        16.01        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       21.44         6.15        19.66        19.73        17.98        16.93 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       19.69        32.12        18.15        13.68        16.93        22.65 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       20.58        19.59        20.19        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       13.71        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        10.09        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         4.37        46.98        44.42        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       37.15        38.24        34.06        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        48.46        60.72        57.53        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99        36.79        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       30.54        13.94        35.21        30.58        14.30        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        5.62        42.51        40.73        15.25        46.03        53.65 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26        31.30        28.67        20.02 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       27.09        32.71        22.03         3.91        23.15        25.41 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 
       15.39        18.64        11.28        34.19        17.65        18.44 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 
       19.82        29.23        29.72        15.19        23.08         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       17.79        23.64        15.65        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       17.56        15.72        14.47         0.36        13.74        20.28 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
        1.58        12.33        20.71        21.40         3.25         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       56.81        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-69-7760 TCGA-69-7761 TCGA-69-7763 
       14.73         5.72         4.64         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        13.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       13.51        14.01        13.45         4.24        19.43         8.42 
TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        6.90        23.38        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
        9.24         1.25        50.33        66.64        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       85.15        49.84        36.66       108.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 
       64.90        22.92         9.57       104.19       238.29        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
       10.55       232.18        39.75        77.59       110.50        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 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        11.61        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        12.23        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7944 TCGA-95-8039 
       23.61         1.08        19.00        41.82        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       25.48        18.54         0.59        15.91        18.67         5.39 
TCGA-97-8175 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-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       36.76         1.45        21.57        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       19.00        14.30        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       49.35        37.35        86.04        58.85         5.49        41.59 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        24.36        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        74.33         0.13         1.64        47.08         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-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          21.44 
[1] "18.7 - 48.6 (28.4)" "0.0 - 238.3 (21.4)"
[1] "hr=" "1.3"
D28V2, continuous
[1] "Remove cluster labels:" "SIP1 MUTATED"          
clus
  SIP1 MUTATED SIP1 WILD-TYPE 
             2            448 
    TCGA-05-4382     TCGA-05-4384     TCGA-05-4396     TCGA-05-4402 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4405     TCGA-05-4410     TCGA-05-4418     TCGA-05-4427 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4434     TCGA-05-5420     TCGA-38-4629     TCGA-38-4630 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-38-4631     TCGA-38-6178     TCGA-38-7271     TCGA-44-2661 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-6146     TCGA-44-6147     TCGA-44-6776     TCGA-44-7661 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-7670     TCGA-44-7671     TCGA-44-8119     TCGA-44-A47F 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-49-4501     TCGA-49-6742     TCGA-49-6745     TCGA-49-6761 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-50-5932     TCGA-50-5935     TCGA-50-6597     TCGA-55-6979 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7284     TCGA-55-7573     TCGA-55-7724     TCGA-55-7725 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7726     TCGA-55-7914     TCGA-55-8090     TCGA-55-8091 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8203     TCGA-55-8204     TCGA-55-8205     TCGA-55-8207 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8511     TCGA-55-8619     TCGA-55-8621     TCGA-55-A48X 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-A491     TCGA-55-A492     TCGA-55-A4DF     TCGA-64-1677 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-67-6217     TCGA-73-4658     TCGA-73-4662     TCGA-73-7498 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7166     TCGA-78-7633     TCGA-78-8660     TCGA-91-6836 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-91-7771     TCGA-91-A4BC     TCGA-93-8067     TCGA-93-A4JQ 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-95-7043     TCGA-95-7562     TCGA-95-7947     TCGA-95-7948 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-95-A4VK     TCGA-95-A4VN     TCGA-97-8172     TCGA-97-A4LX 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-97-A4M2     TCGA-97-A4M3     TCGA-97-A4M7     TCGA-J2-8192 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-J2-8194     TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-MP-A4T8     TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-MP-A4TD 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4244     TCGA-05-4249     TCGA-05-4250     TCGA-05-4389 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4390     TCGA-05-4395     TCGA-05-4397     TCGA-05-4398 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4403     TCGA-05-4415     TCGA-05-4417     TCGA-05-4420 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4422     TCGA-05-4424     TCGA-05-4425     TCGA-05-4426 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4430     TCGA-05-4432     TCGA-05-4433     TCGA-05-5423 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-5425     TCGA-05-5428     TCGA-05-5429     TCGA-05-5715 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-38-4625 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-38-4626     TCGA-38-4627     TCGA-38-4628     TCGA-38-4632 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-38-A44F     TCGA-44-2656     TCGA-44-2657     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-44-6148     TCGA-44-6774     TCGA-44-6775 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-6777     TCGA-44-6778     TCGA-44-6779     TCGA-44-7659 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-7660     TCGA-44-7662     TCGA-44-7667     TCGA-44-7669 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-7672     TCGA-44-8117     TCGA-44-8120     TCGA-44-A479 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-A47A     TCGA-44-A47B     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-49-4505     TCGA-49-4506 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-49-4507     TCGA-49-4510     TCGA-49-4512     TCGA-49-4514 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-49-6743     TCGA-49-6744     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-50-5933     TCGA-50-5936     TCGA-50-5939 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-50-5941     TCGA-50-5942     TCGA-50-5944     TCGA-50-5946 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-50-6590     TCGA-50-6591     TCGA-50-6592     TCGA-50-6593 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-50-6594     TCGA-50-6595     TCGA-50-6673     TCGA-50-7109 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-50-8457     TCGA-50-8459     TCGA-50-8460     TCGA-53-7624 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-53-7626     TCGA-53-7813     TCGA-53-A4EZ     TCGA-55-6642 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-6968     TCGA-55-6969     TCGA-55-6970     TCGA-55-6971 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-6972     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-55-7570 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7574     TCGA-55-7576     TCGA-55-7727     TCGA-55-7728 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7815     TCGA-55-7816     TCGA-55-7903     TCGA-55-7907 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7910     TCGA-55-7911     TCGA-55-7913     TCGA-55-7994 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7995     TCGA-55-8085     TCGA-55-8087     TCGA-55-8089 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8092     TCGA-55-8094     TCGA-55-8096     TCGA-55-8097 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8206     TCGA-55-8208     TCGA-55-8299     TCGA-55-8301 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8302     TCGA-55-8505     TCGA-55-8506     TCGA-55-8507 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8508     TCGA-55-8510     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-55-8620     TCGA-55-A48Y     TCGA-55-A48Z     TCGA-55-A490 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-A493     TCGA-55-A494     TCGA-55-A4DG     TCGA-62-8394 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-62-8395     TCGA-62-8397     TCGA-62-8398     TCGA-62-8399 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-62-8402     TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-62-A46S     TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-62-A470     TCGA-62-A471     TCGA-62-A472     TCGA-64-1676 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-64-1679     TCGA-64-1681     TCGA-64-5774     TCGA-64-5775 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-64-5778     TCGA-64-5779     TCGA-64-5781     TCGA-64-5815 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-67-3771     TCGA-67-3772     TCGA-67-3773     TCGA-67-4679 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-67-6215     TCGA-67-6216     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-73-4659     TCGA-73-4666 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4670     TCGA-73-4675     TCGA-73-4676 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-73-4677     TCGA-73-7499     TCGA-78-7143     TCGA-78-7145 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7146     TCGA-78-7147     TCGA-78-7148     TCGA-78-7149 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7150     TCGA-78-7152     TCGA-78-7153     TCGA-78-7154 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7155     TCGA-78-7156     TCGA-78-7158     TCGA-78-7159 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7160     TCGA-78-7161     TCGA-78-7162     TCGA-78-7163 
"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-78-8640     TCGA-78-8648     TCGA-78-8655     TCGA-78-8662 
"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-86-8585 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8668     TCGA-86-8669     TCGA-86-8671     TCGA-86-8672 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8673     TCGA-86-8674     TCGA-86-A456     TCGA-86-A4JF 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-A4P7     TCGA-86-A4P8     TCGA-91-6828     TCGA-91-6829 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-91-6830     TCGA-91-6831     TCGA-91-6835     TCGA-91-6840 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-91-6847     TCGA-91-6848     TCGA-91-6849     TCGA-91-8496 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-91-8497     TCGA-91-8499     TCGA-91-A4BD     TCGA-93-7347 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-93-7348     TCGA-93-A4JN     TCGA-93-A4JO     TCGA-93-A4JP 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-95-7039     TCGA-95-7944     TCGA-95-8039     TCGA-95-8494 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-95-A4VP     TCGA-97-7546     TCGA-97-7547     TCGA-97-7552 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-97-7553     TCGA-97-7554     TCGA-97-7937     TCGA-97-7938 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-97-7941     TCGA-97-8171     TCGA-97-8174     TCGA-97-8175 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-97-8176     TCGA-97-8177     TCGA-97-8179     TCGA-97-8547 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-97-8552     TCGA-97-A4M0     TCGA-97-A4M1     TCGA-97-A4M5 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-97-A4M6     TCGA-99-7458     TCGA-99-8025     TCGA-99-8028 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-99-8032     TCGA-99-8033     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-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-A4T9     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-A4YF 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-NJ-A4YG     TCGA-NJ-A4YI     TCGA-NJ-A4YP     TCGA-NJ-A4YQ 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-NJ-A55A     TCGA-NJ-A55O     TCGA-NJ-A55R     TCGA-O1-A52J 
"SIP1 WILD-TYPE" "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      118      132        46        65         70
                vv
clus             STAGE IIIB STAGE IV
  SIP1 MUTATED            0        0
  SIP1 WILD-TYPE         11       24
D28V3, multiclass
            clus
vv           SIP1 MUTATED SIP1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              3            118
  STAGE IB              0            132
  STAGE IIA             0             46
  STAGE IIB             1             65
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             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
  SIP1 MUTATED     2   2   0   0
  SIP1 WILD-TYPE 154 259  43  18
D28V4, multiclass
    clus
vv   SIP1 MUTATED SIP1 WILD-TYPE
  T1            2            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
  SIP1 MUTATED     3   1     0
  SIP1 WILD-TYPE 305  88    72
D28V5, multiclass
       clus
vv      SIP1 MUTATED SIP1 WILD-TYPE
  N0               3            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"
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 258 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIP1 MUTATED      2    2
  SIP1 WILD-TYPE  258  219
        clus
vv       SIP1 MUTATED SIP1 WILD-TYPE
  FEMALE            2            258
  MALE              2            219
[1] 2 2
[1] FALSE
D28V8, binary
                cls
clus               0   1
  SIP1 MUTATED     4   0
  SIP1 WILD-TYPE 380  55
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIP1 MUTATED      4    0
  SIP1 WILD-TYPE  380   55
     clus
vv    SIP1 MUTATED SIP1 WILD-TYPE
  NO             4            380
  YES            0             55
[1] 2 2
[1] FALSE
D28V9, continuous
[1] "Remove cluster labels:" "SIP1 MUTATED"          
clus
  SIP1 MUTATED SIP1 WILD-TYPE 
             1            121 
    TCGA-44-6147     TCGA-44-A47F     TCGA-49-6742     TCGA-55-7573 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7725     TCGA-55-7914     TCGA-55-8205     TCGA-55-8511 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8621     TCGA-55-A491     TCGA-55-A492 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-64-1677     TCGA-73-4662     TCGA-73-7498     TCGA-93-8067 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-35-4122     TCGA-35-4123     TCGA-35-5375 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-3396     TCGA-44-3918     TCGA-44-4112     TCGA-44-6144 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-44-6775     TCGA-44-7660     TCGA-49-4486     TCGA-49-4494 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-49-4505     TCGA-49-4506     TCGA-49-4510     TCGA-49-6743 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-49-6744     TCGA-53-7624     TCGA-53-A4EZ     TCGA-55-5899 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7574     TCGA-55-7910     TCGA-55-7913 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7995     TCGA-55-8089     TCGA-55-8096     TCGA-55-8208 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8507     TCGA-55-8508     TCGA-55-8512     TCGA-55-8513 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8620     TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A494 
"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-64-1681     TCGA-64-5775     TCGA-64-5778     TCGA-69-7974 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-69-8254     TCGA-71-6725     TCGA-71-8520     TCGA-73-4659 
"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-73-7499     TCGA-75-5122     TCGA-83-5908 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-6562     TCGA-86-6851     TCGA-86-7701     TCGA-86-7711 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-7713     TCGA-86-7714     TCGA-86-7953     TCGA-86-7954 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-7955     TCGA-86-8054     TCGA-86-8055     TCGA-86-8056 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8073     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8280     TCGA-86-8281 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8358     TCGA-86-8359     TCGA-86-8668     TCGA-86-8669 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8671     TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-91-6829     TCGA-91-6849     TCGA-93-7347     TCGA-93-7348 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-93-A4JN     TCGA-93-A4JO     TCGA-99-7458     TCGA-MN-A4N4 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-MN-A4N5 
"SIP1 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SIP1 MUTATED                            0                                 1
  SIP1 WILD-TYPE                         17                               101
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SIP1 MUTATED                                                    2
  SIP1 WILD-TYPE                                                294
                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                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            294
  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 310  12   4  25
D28V13, multiclass
[1] "Remove cluster labels:" "SIP1 MUTATED"          
clus
  SIP1 MUTATED SIP1 WILD-TYPE 
             2            351 
    TCGA-05-4382     TCGA-05-4384     TCGA-05-4396     TCGA-05-4402 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4405     TCGA-05-4410     TCGA-05-4418     TCGA-05-4427 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4434     TCGA-05-5420     TCGA-38-4629     TCGA-38-4630 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-38-4631     TCGA-38-6178     TCGA-38-7271     TCGA-44-2661 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-49-4501     TCGA-49-6742     TCGA-49-6761     TCGA-50-6597 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7284     TCGA-55-7724     TCGA-55-7725     TCGA-55-7726 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7914     TCGA-55-8090     TCGA-55-8091     TCGA-55-8203 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8204     TCGA-55-8205     TCGA-55-8207     TCGA-55-8511 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8621     TCGA-55-A48X     TCGA-55-A491 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-A492     TCGA-55-A4DF     TCGA-64-1677     TCGA-67-6217 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-73-4658     TCGA-73-4662     TCGA-73-7498     TCGA-78-7166 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7633     TCGA-78-8660     TCGA-80-5607     TCGA-80-5611 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-93-8067     TCGA-93-A4JQ     TCGA-95-7562     TCGA-95-7947 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-95-7948     TCGA-95-A4VK     TCGA-95-A4VN     TCGA-97-A4M2 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-97-A4M7     TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-MP-A4T8     TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-MP-A4TD 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4244     TCGA-05-4249     TCGA-05-4250     TCGA-05-4389 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4390     TCGA-05-4395     TCGA-05-4397     TCGA-05-4398 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4403     TCGA-05-4415     TCGA-05-4417     TCGA-05-4420 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4422     TCGA-05-4424     TCGA-05-4425     TCGA-05-4426 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-4430     TCGA-05-4432     TCGA-05-4433     TCGA-05-5423 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-05-5425     TCGA-05-5428     TCGA-05-5429     TCGA-05-5715 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-35-4122     TCGA-35-4123     TCGA-35-5375     TCGA-38-4625 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-38-4626     TCGA-38-4627     TCGA-38-4628     TCGA-38-4632 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-38-A44F     TCGA-44-2657     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-49-4505 
"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-49-6744     TCGA-49-6767     TCGA-50-5051 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-50-5055     TCGA-50-5066     TCGA-50-5931     TCGA-50-5942 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-50-5944     TCGA-50-6593     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-55-6712     TCGA-55-6970     TCGA-55-6971 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-6972     TCGA-55-6980     TCGA-55-6981     TCGA-55-6983 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-6985     TCGA-55-7227     TCGA-55-7281     TCGA-55-7570 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7574     TCGA-55-7576     TCGA-55-7727     TCGA-55-7728 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7815     TCGA-55-7903     TCGA-55-7907     TCGA-55-7910 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-7911     TCGA-55-7913     TCGA-55-7994     TCGA-55-7995 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8085     TCGA-55-8087     TCGA-55-8089     TCGA-55-8092 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8094     TCGA-55-8097     TCGA-55-8206     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-55-8512     TCGA-55-8513     TCGA-55-8514     TCGA-55-8614 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-8615     TCGA-55-8616     TCGA-55-8620     TCGA-55-A48Y 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A493     TCGA-55-A494 
"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-64-1679     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-71-6725 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     TCGA-73-4666     TCGA-73-4668 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-73-4670     TCGA-73-4675     TCGA-73-4676     TCGA-73-4677 
"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-78-7167 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7220     TCGA-78-7535     TCGA-78-7536     TCGA-78-7537 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-7539     TCGA-78-7540     TCGA-78-7542     TCGA-78-8640 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-78-8648     TCGA-78-8655     TCGA-78-8662     TCGA-80-5608 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-6562     TCGA-86-7701     TCGA-86-7711 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-7713     TCGA-86-7714     TCGA-86-7953     TCGA-86-7954 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-7955     TCGA-86-8054     TCGA-86-8055     TCGA-86-8056 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8073     TCGA-86-8074     TCGA-86-8075     TCGA-86-8076 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-86-8278     TCGA-86-8279     TCGA-86-8280     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-91-6828 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-91-6829     TCGA-91-6835     TCGA-91-6840     TCGA-91-A4BD 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-93-7347     TCGA-93-7348     TCGA-93-A4JN     TCGA-93-A4JO 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-93-A4JP     TCGA-95-7944     TCGA-95-8039     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-99-7458     TCGA-99-8025     TCGA-99-8028     TCGA-99-8032 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-99-8033     TCGA-J2-A4AD     TCGA-J2-A4AE     TCGA-J2-A4AG 
"SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" "SIP1 WILD-TYPE" 
    TCGA-L4-A4E5     TCGA-L4-A4E6     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-A4T9 
"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-A4YQ 
"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                        30   375
D28V14, multiclass
                                  clus
vv                                 SIP1 MUTATED SIP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1              6
  BLACK OR AFRICAN AMERICAN                   0             30
  WHITE                                       3            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"
D28V15, binary
                cls
clus               0   1
  SIP1 MUTATED     0   4
  SIP1 WILD-TYPE   6 347
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIP1 MUTATED      0    4
  SIP1 WILD-TYPE    6  347
                        clus
vv                       SIP1 MUTATED SIP1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            4            347
[1] 2 2
[1] FALSE

Clustering(29) Variable = SLC4A3 MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2                0   1
  SLC4A3 MUTATED    11   7
  SLC4A3 WILD-TYPE 287 164
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
              18              451 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
               7              164 
$`SLC4A3 MUTATED`
TCGA-55-8205 TCGA-95-7043 TCGA-MP-A4TA TCGA-44-2656 TCGA-44-5644 TCGA-49-4488 
       19.69        16.54        31.23        46.98        28.37        28.57 
TCGA-50-5066 TCGA-50-5946 TCGA-62-A46R TCGA-64-5778 TCGA-64-5781 TCGA-69-7978 
       47.41        53.16        56.71        42.90        51.25         4.41 
TCGA-69-7980 TCGA-78-7156 TCGA-78-7536 TCGA-91-6840 TCGA-95-7567 TCGA-MP-A4SY 
       13.51        32.09         8.02        12.23        18.67        49.35 

$`SLC4A3 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       17.98        16.93        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD 
        6.35        10.09        27.19         5.29         2.43        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       47.05        19.00         2.99        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-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-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       44.61         4.37        44.42        42.77        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 
       34.06        33.73        26.56        33.30        28.01        23.77 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       19.56        23.15        21.63        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        22.72        19.46         7.17        36.07        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         8.55        15.98        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 
       11.54        13.64        13.45        76.21        28.11        12.66 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       35.54        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       55.89        53.29        55.33        22.26        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
      101.72        15.72        60.16        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       14.27        78.67         8.45        15.12        48.46        60.72 
TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       57.53        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 
       34.29        30.54        13.94        35.21        30.58        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       80.52         5.62        42.51        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       53.65         3.88        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26        31.30        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       20.02        27.09        32.71        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       25.41        15.39        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.44        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42        17.56        15.72        14.47         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       14.66         1.58        12.33        20.71        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        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-A46S 
       14.60        88.64        49.25        47.80        19.53        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 
       56.81        81.80        38.37        87.98         2.04        28.41 
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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        7.56         6.05        13.41        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       19.43         8.42         6.90        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 
        4.31        30.31         9.24         1.25        50.33        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       77.85        43.82        85.15        49.84        36.66       108.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
      100.57       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-78-7167 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-78-8662 TCGA-80-5608 
       10.55       232.18        39.75        77.59       110.50        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 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        11.61        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
       10.19         2.60        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
        1.08        19.00        41.82        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       15.39        16.41        14.30        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       19.76        20.84        18.67        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        1.45        21.57        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
       14.30        38.63         2.76        86.14        58.45        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        47.08         0.49         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
            4.41             0.00 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
           56.71           238.29 
  SLC4A3 MUTATED SLC4A3 WILD-TYPE 
           29.90            21.44 
[1] "4.4 - 56.7 (29.9)"  "0.0 - 238.3 (21.4)"
[1] "hr=" "1.1"
D29V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  SLC4A3 MUTATED         1        5        6         1         3          1
  SLC4A3 WILD-TYPE       3      116      126        45        63         69
                  vv
clus               STAGE IIIB STAGE IV
  SLC4A3 MUTATED            0        1
  SLC4A3 WILD-TYPE         11       23
D29V3, multiclass
            clus
vv           SLC4A3 MUTATED SLC4A3 WILD-TYPE
  STAGE I                 1                3
  STAGE IA                5              116
  STAGE IB                6              126
  STAGE IIA               1               45
  STAGE IIB               3               63
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                1               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
  SLC4A3 MUTATED     6  11   0   1
  SLC4A3 WILD-TYPE 150 250  43  17
D29V4, multiclass
    clus
vv   SLC4A3 MUTATED SLC4A3 WILD-TYPE
  T1              6              150
  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 295  85    71
D29V5, multiclass
       clus
vv      SLC4A3 MUTATED SLC4A3 WILD-TYPE
  N0                13              295
  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 251 212
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED      9    9
  SLC4A3 WILD-TYPE  251  212
        clus
vv       SLC4A3 MUTATED SLC4A3 WILD-TYPE
  FEMALE              9              251
  MALE                9              212
[1] 2 2
[1] FALSE
D29V8, binary
                  cls
clus                 0   1
  SLC4A3 MUTATED    17   1
  SLC4A3 WILD-TYPE 367  54
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED     17    1
  SLC4A3 WILD-TYPE  367   54
     clus
vv    SLC4A3 MUTATED SLC4A3 WILD-TYPE
  NO              17              367
  YES              1               54
[1] 2 2
[1] FALSE
D29V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SLC4A3 MUTATED                            0                                 8
  SLC4A3 WILD-TYPE                         17                                94
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SLC4A3 MUTATED                                                    9
  SLC4A3 WILD-TYPE                                                287
                  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                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                94
  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                                    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 301  12   4  25
D29V13, multiclass
    clus
vv   SLC4A3 MUTATED SLC4A3 WILD-TYPE
  R0             11              301
  R1              0               12
  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                        29   361
D29V14, multiclass
                                  clus
vv                                 SLC4A3 MUTATED SLC4A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               29
  WHITE                                        17              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"
D29V15, binary
                  cls
clus                 0   1
  SLC4A3 MUTATED     0  15
  SLC4A3 WILD-TYPE   6 336
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A3 MUTATED      0   15
  SLC4A3 WILD-TYPE    6  336
                        clus
vv                       SLC4A3 MUTATED SLC4A3 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             15              336
[1] 2 2
[1] FALSE

Clustering(30) Variable = STK19 MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2               0   1
  STK19 MUTATED     3   2
  STK19 WILD-TYPE 295 169
  STK19 MUTATED STK19 WILD-TYPE 
              5             464 
  STK19 MUTATED STK19 WILD-TYPE 
              2             169 
$`STK19 MUTATED`
TCGA-55-8506 TCGA-62-A46Y TCGA-69-7979 TCGA-86-8671 TCGA-MP-A4TF 
        0.36        13.61        13.41        27.58        11.05 

$`STK19 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       17.29        16.54         2.86        15.68        15.65        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       18.18        17.92        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 
       24.30        23.80         6.35        10.09        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 
       31.23         2.43        10.09        50.07         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       37.02         0.00        24.03        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        24.00         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-38-4632 TCGA-38-A44F TCGA-44-2656 
      120.79        37.71        49.05        44.61         4.37        46.98 
TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        23.18        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       22.72        19.46         7.17        36.07        18.87        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       12.66         8.55        15.98        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       35.54        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       55.89        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 
      101.72        15.72        60.16        47.41        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        9.27        14.27        78.67         8.45        15.12        48.46 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       60.72        57.53        53.16        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05        12.16         6.21         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.79        27.25        34.29        30.54        13.94        35.21 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       30.58        14.30        80.52         5.62        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       15.25        46.03        53.65         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       31.30        28.67        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        3.91        23.15        25.41        15.39        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       34.19        17.65        18.44        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       15.19        23.08         5.06        17.79        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       29.19        22.16        15.42        17.56        15.72        14.47 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       13.74        20.28        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.62        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        3.25         0.92        15.81        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       29.92        56.81        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-69-7760 TCGA-69-7761 
       14.04        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       13.51        14.01        13.45         4.24        19.43         8.42 
TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        6.90        23.38        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
        9.24         1.25        50.33        66.64        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       85.15        49.84        36.66       108.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 
       64.90        22.92         9.57       104.19       238.29        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
       10.55       232.18        39.75        77.59       110.50        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 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        11.61        13.91 
TCGA-86-8669 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       30.84         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
        1.08        19.00        41.82        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       25.48        18.54         0.59        15.91        18.67         5.39 
TCGA-97-8175 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-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       36.76         1.45        21.57        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       19.00        14.30        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       49.35        37.35        86.04        58.85         5.49        41.59 
TCGA-MP-A4TE TCGA-MP-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 
       74.33         0.13         1.64        47.08         0.49         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 
          13.41           21.52 
[1] "0.4 - 27.6 (13.4)"  "0.0 - 238.3 (21.5)"
[1] "hr=" "2.8"
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      121      131        45        64         69
                 vv
clus              STAGE IIIB STAGE IV
  STK19 MUTATED            0        0
  STK19 WILD-TYPE         11       24
D30V3, multiclass
            clus
vv           STK19 MUTATED STK19 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0             121
  STAGE IB               1             131
  STAGE IIA              1              45
  STAGE IIB              2              64
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              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
  STK19 MUTATED     0   4   1   0
  STK19 WILD-TYPE 156 257  42  18
D30V4, multiclass
    clus
vv   STK19 MUTATED STK19 WILD-TYPE
  T1             0             156
  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 305  88    71
D30V5, multiclass
       clus
vv      STK19 MUTATED STK19 WILD-TYPE
  N0                3             305
  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 255 221
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      5    0
  STK19 WILD-TYPE  255  221
        clus
vv       STK19 MUTATED STK19 WILD-TYPE
  FEMALE             5             255
  MALE               0             221
[1] 2 2
[1] FALSE
D30V8, binary
                 cls
clus                0   1
  STK19 MUTATED     3   1
  STK19 WILD-TYPE 381  54
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      3    1
  STK19 WILD-TYPE  381   54
     clus
vv    STK19 MUTATED STK19 WILD-TYPE
  NO              3             381
  YES             1              54
[1] 2 2
[1] FALSE
D30V9, continuous
[1] "Remove cluster labels:" "STK19 MUTATED"         
clus
  STK19 MUTATED STK19 WILD-TYPE 
              2             120 
     TCGA-44-6147      TCGA-44-A47F      TCGA-49-6742      TCGA-55-7573 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7914      TCGA-55-8205      TCGA-55-8511 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8621      TCGA-55-A491      TCGA-55-A492 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-64-1677      TCGA-73-4662      TCGA-73-7498      TCGA-93-8067 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-35-4122      TCGA-35-4123      TCGA-35-5375 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-3396      TCGA-44-3918      TCGA-44-4112      TCGA-44-6144 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-7660      TCGA-49-4486      TCGA-49-4494 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-49-4505      TCGA-49-4506      TCGA-49-4510      TCGA-49-6743 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-49-6744      TCGA-53-7624      TCGA-53-A4EZ      TCGA-55-5899 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7574      TCGA-55-7910      TCGA-55-7913 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-7995      TCGA-55-8089      TCGA-55-8096      TCGA-55-8208 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8512      TCGA-55-8513 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A494 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-62-8394      TCGA-62-8395      TCGA-62-8397      TCGA-62-8398 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-62-8399      TCGA-62-8402      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-A46U      TCGA-62-A46V 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-62-A470      TCGA-62-A471      TCGA-62-A472      TCGA-64-1681 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-64-5775      TCGA-64-5778      TCGA-69-7974      TCGA-69-8254 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-71-6725      TCGA-71-8520      TCGA-73-4659      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-73-7499      TCGA-75-5122      TCGA-83-5908      TCGA-86-6562 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-6851      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7953      TCGA-86-7954      TCGA-86-7955 
"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-86-8075      TCGA-86-8076      TCGA-86-8278 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8280      TCGA-86-8281      TCGA-86-8358 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-A456 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6829      TCGA-91-6849 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-93-7347      TCGA-93-7348      TCGA-93-A4JN      TCGA-93-A4JO 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-95-7567      TCGA-99-7458      TCGA-MN-A4N4      TCGA-MN-A4N5 
"STK19 WILD-TYPE" "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                         16                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  STK19 MUTATED                                                    2
  STK19 WILD-TYPE                                                294
                 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                                      16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             294
  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             330 
     TCGA-05-4382      TCGA-05-4384      TCGA-05-4396      TCGA-05-4405 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-4410      TCGA-05-4418      TCGA-05-4427      TCGA-05-4434 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-5420      TCGA-38-4629      TCGA-38-4631      TCGA-38-7271 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-6146      TCGA-44-6776      TCGA-44-7661      TCGA-44-7670 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-8119      TCGA-44-A47F      TCGA-49-6742      TCGA-49-6745 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-49-6761      TCGA-55-7724      TCGA-55-7725      TCGA-55-7726 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-7914      TCGA-55-8203      TCGA-55-8205      TCGA-55-8511 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8621      TCGA-55-A48X      TCGA-55-A491      TCGA-55-A492 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-A4DF      TCGA-64-1677      TCGA-73-4658      TCGA-73-4662 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-73-7498      TCGA-78-7166      TCGA-78-7633      TCGA-78-8660 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-80-5607      TCGA-80-5611      TCGA-91-6836      TCGA-91-7771 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-91-A4BC      TCGA-93-8067      TCGA-95-7043      TCGA-95-7562 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-95-7947      TCGA-95-7948      TCGA-95-A4VK      TCGA-95-A4VN 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-97-8172      TCGA-97-A4LX      TCGA-97-A4M2      TCGA-97-A4M3 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-97-A4M7      TCGA-J2-8194      TCGA-L9-A443      TCGA-L9-A444 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-MP-A4T8      TCGA-MP-A4TA      TCGA-MP-A4TC      TCGA-MP-A4TD 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-4244      TCGA-05-4249      TCGA-05-4250      TCGA-05-4389 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-4390      TCGA-05-4397      TCGA-05-4398      TCGA-05-4415 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-4417      TCGA-05-4420      TCGA-05-4422      TCGA-05-4424 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-4425      TCGA-05-4426      TCGA-05-4430      TCGA-05-4432 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-05-4433      TCGA-05-5423      TCGA-05-5425      TCGA-05-5428 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-35-4122      TCGA-35-4123      TCGA-35-5375      TCGA-38-4625 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-38-4626      TCGA-38-4632      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-44-6148      TCGA-44-6774 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-6777      TCGA-44-6778      TCGA-44-6779 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-7659      TCGA-44-7660      TCGA-44-7662      TCGA-44-7667 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-7669      TCGA-44-7672      TCGA-44-8117      TCGA-44-8120 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-A479      TCGA-44-A47A      TCGA-44-A47B      TCGA-44-A47G 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-44-A4SS      TCGA-44-A4SU      TCGA-49-4486      TCGA-49-4487 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-49-4490      TCGA-49-4494      TCGA-49-4505      TCGA-49-4506 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-49-4507      TCGA-49-4510      TCGA-49-4514      TCGA-49-6743 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-49-6744      TCGA-49-6767      TCGA-50-5051      TCGA-50-5072 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-50-5931      TCGA-50-5939      TCGA-50-5941      TCGA-50-5942 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-50-6590      TCGA-50-7109      TCGA-50-8457      TCGA-50-8459 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-53-7624      TCGA-53-7626      TCGA-53-7813      TCGA-53-A4EZ 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-6543      TCGA-55-6971      TCGA-55-6983      TCGA-55-6985 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-7281      TCGA-55-7283      TCGA-55-7574      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-55-7913      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-55-8208      TCGA-55-8299      TCGA-55-8301      TCGA-55-8302 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8512      TCGA-55-8514      TCGA-55-8614 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-8615      TCGA-55-8620      TCGA-55-A48Y      TCGA-55-A48Z 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A493      TCGA-55-A494      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-64-1679      TCGA-64-5774 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-64-5775      TCGA-64-5778      TCGA-64-5779      TCGA-64-5781 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-64-5815      TCGA-69-7761      TCGA-69-7763      TCGA-69-7764 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-69-7973      TCGA-69-7974      TCGA-69-7978      TCGA-69-7980 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-69-8253      TCGA-69-8254      TCGA-69-8255      TCGA-69-A59K 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-73-4659      TCGA-73-4666      TCGA-73-4668      TCGA-73-4670 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-73-4675      TCGA-73-4676      TCGA-75-5122      TCGA-75-5125 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-75-5126      TCGA-75-6206      TCGA-75-6207      TCGA-75-6211 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-75-6214      TCGA-75-7027      TCGA-75-7031      TCGA-78-7145 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-7146      TCGA-78-7147      TCGA-78-7148      TCGA-78-7149 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-7150      TCGA-78-7152      TCGA-78-7153      TCGA-78-7154 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-7155      TCGA-78-7156      TCGA-78-7158      TCGA-78-7159 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-7160      TCGA-78-7161      TCGA-78-7162      TCGA-78-7163 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-7167      TCGA-78-7220      TCGA-78-7535      TCGA-78-7536 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-7537      TCGA-78-7539      TCGA-78-7542      TCGA-78-8640 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-78-8648      TCGA-78-8655      TCGA-78-8662      TCGA-80-5608 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-6851      TCGA-86-7711      TCGA-86-7714 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-7954      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-86-8281      TCGA-86-8358 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8669      TCGA-86-8673      TCGA-86-8674 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-91-6829      TCGA-91-6830      TCGA-91-6835      TCGA-91-6840 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-91-6849      TCGA-91-8499      TCGA-93-7347      TCGA-93-7348 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-95-7039      TCGA-95-7944 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-95-A4VP      TCGA-97-7546      TCGA-97-7547      TCGA-97-7552 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-97-7553      TCGA-97-7554      TCGA-97-7937      TCGA-97-7938 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-97-7941      TCGA-97-8171      TCGA-97-8174      TCGA-97-8176 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-97-8179      TCGA-97-A4M0      TCGA-97-A4M1      TCGA-97-A4M5 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-99-7458      TCGA-99-8025      TCGA-99-8028      TCGA-99-8032 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-J2-A4AD      TCGA-J2-A4AG      TCGA-L4-A4E5      TCGA-L4-A4E6 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-MP-A4SV      TCGA-MP-A4SW      TCGA-MP-A4SY      TCGA-MP-A4T2 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-MP-A4T4      TCGA-MP-A4T6      TCGA-MP-A4T7      TCGA-MP-A4T9 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-MP-A4TE      TCGA-MP-A4TH      TCGA-MP-A4TI      TCGA-MP-A4TK 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-MP-A5C7      TCGA-NJ-A4YF      TCGA-NJ-A4YG      TCGA-NJ-A4YI 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-NJ-A4YP      TCGA-NJ-A4YQ      TCGA-NJ-A55A      TCGA-NJ-A55O 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" "STK19 WILD-TYPE" 
     TCGA-NJ-A55R      TCGA-O1-A52J 
"STK19 WILD-TYPE" "STK19 WILD-TYPE" 
D30V12, continuous
                 vv
clus               R0  R1  R2  RX
  STK19 MUTATED     4   0   0   0
  STK19 WILD-TYPE 308  12   4  25
D30V13, multiclass
    clus
vv   STK19 MUTATED STK19 WILD-TYPE
  R0             4             308
  R1             0              12
  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                        30   373
D30V14, multiclass
                                  clus
vv                                 STK19 MUTATED STK19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              30
  WHITE                                        5             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"
D30V15, binary
                 cls
clus                0   1
  STK19 MUTATED     0   5
  STK19 WILD-TYPE   6 346
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK19 MUTATED      0    5
  STK19 WILD-TYPE    6  346
                        clus
vv                       STK19 MUTATED STK19 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             5             346
[1] 2 2
[1] FALSE

Clustering(31) Variable = NUDT11 MUTATION ANALYSIS
D31V1, survival
                  sevent
clus2                0   1
  NUDT11 MUTATED     4   1
  NUDT11 WILD-TYPE 294 170
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               5              464 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               1              170 
$`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-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       18.31        29.00         9.37        46.72        16.04        17.16 
TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 
       11.64        40.60        21.47        41.69        23.05        48.62 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        5.79         7.79         7.99        16.01        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       21.44         6.15        19.66        19.73        17.98        16.93 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       19.69        32.12        18.15        13.68        16.93        22.65 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       20.58        19.59        20.19        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       13.71        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        10.09        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         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-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       55.33        22.26        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        48.46        60.72        57.53        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99        36.79        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       30.54        13.94        35.21        30.58        14.30        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        5.62        42.51        40.73        15.25        46.03        53.65 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26        31.30        28.67        20.02 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       27.09        32.71        22.03         3.91        23.15        25.41 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 
       15.39        18.64        11.28        34.19        17.65        18.44 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 
       19.82        29.23        29.72        15.19        23.08         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       17.79        23.64        15.65        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       17.56        15.72        14.47         0.36        13.74        20.28 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
        1.58        12.33        20.71        21.40         3.25         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       56.81        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-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        19.43         8.42         6.90 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       23.38        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
        1.25        50.33        66.64        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       49.84        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
       22.92         9.57       104.19       238.29        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
       24.33         0.79        22.82        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-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-91-8496 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.18        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
       19.00        41.82        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       15.39        16.41        14.30        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       19.76        20.84        18.67        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        1.45        21.57        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       14.30        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE 
       37.35        86.04        58.85         5.49        41.59        29.46 
TCGA-MP-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 
       74.33         0.13         1.64        47.08         0.49         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 
          29.230           21.455 
[1] "11.1 - 78.7 (29.2)" "0.0 - 238.3 (21.5)"
[1] "hr=" "2.1"
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      120      131        46        65         70
                  vv
clus               STAGE IIIB STAGE IV
  NUDT11 MUTATED            1        0
  NUDT11 WILD-TYPE         10       24
D31V3, multiclass
            clus
vv           NUDT11 MUTATED NUDT11 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                1              120
  STAGE IB                1              131
  STAGE IIA               0               46
  STAGE IIB               1               65
  STAGE IIIA              0               70
  STAGE IIIB              1               10
  STAGE IV                0               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
  NUDT11 MUTATED     1   2   1   1
  NUDT11 WILD-TYPE 155 259  42  17
D31V4, multiclass
    clus
vv   NUDT11 MUTATED NUDT11 WILD-TYPE
  T1              1              155
  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 305  88    71
D31V5, multiclass
       clus
vv      NUDT11 MUTATED NUDT11 WILD-TYPE
  N0                 3              305
  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 260 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      0    5
  NUDT11 WILD-TYPE  260  216
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  FEMALE              0              260
  MALE                5              216
[1] 2 2
[1] FALSE
D31V8, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     3   1
  NUDT11 WILD-TYPE 381  54
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      3    1
  NUDT11 WILD-TYPE  381   54
     clus
vv    NUDT11 MUTATED NUDT11 WILD-TYPE
  NO               3              381
  YES              1               54
[1] 2 2
[1] FALSE
D31V9, continuous
[1] "Remove cluster labels:" "NUDT11 MUTATED"        
clus
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               2              120 
      TCGA-44-6147       TCGA-49-6742       TCGA-55-7573       TCGA-55-7725 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7914       TCGA-55-8205       TCGA-55-8511       TCGA-55-8619 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8621       TCGA-55-A491       TCGA-55-A492       TCGA-64-1677 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-73-4662       TCGA-73-7498       TCGA-93-8067       TCGA-MN-A4N1 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      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-44-6775 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-7660       TCGA-49-4486       TCGA-49-4494       TCGA-49-4505 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-49-4506       TCGA-49-4510       TCGA-49-6743       TCGA-49-6744 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-53-7624       TCGA-53-A4EZ       TCGA-55-5899       TCGA-55-7283 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7574       TCGA-55-7910       TCGA-55-7913       TCGA-55-7995 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8089       TCGA-55-8096       TCGA-55-8208       TCGA-55-8507 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8508       TCGA-55-8512       TCGA-55-8513       TCGA-55-8620 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A494       TCGA-62-8394 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-62-8395       TCGA-62-8397       TCGA-62-8398       TCGA-62-8399 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-62-8402       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-A46U       TCGA-62-A46V       TCGA-62-A46Y 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-62-A470       TCGA-62-A471       TCGA-62-A472       TCGA-64-1681 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-64-5775       TCGA-64-5778       TCGA-69-7974       TCGA-69-8254 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-71-6725       TCGA-71-8520       TCGA-73-4659       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-73-7499       TCGA-75-5122       TCGA-83-5908       TCGA-86-6562 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-6851       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7953       TCGA-86-7954       TCGA-86-7955 
"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-86-8075       TCGA-86-8278       TCGA-86-8279 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8280       TCGA-86-8281       TCGA-86-8358       TCGA-86-8359 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8668       TCGA-86-8669       TCGA-86-8671       TCGA-86-A456 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6829       TCGA-91-6849 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-93-7347       TCGA-93-7348       TCGA-93-A4JN       TCGA-93-A4JO 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-95-7567       TCGA-99-7458       TCGA-MN-A4N4       TCGA-MN-A4N5 
"NUDT11 WILD-TYPE" "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                         17                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NUDT11 MUTATED                                                    3
  NUDT11 WILD-TYPE                                                293
                  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                                       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                                    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              331 
      TCGA-05-4382       TCGA-05-4384       TCGA-05-4396       TCGA-05-4405 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4410       TCGA-05-4418       TCGA-05-4427       TCGA-05-4434 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-5420       TCGA-38-4629       TCGA-38-4631       TCGA-38-7271 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-6146       TCGA-44-6776       TCGA-44-7661       TCGA-44-7670 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-8119       TCGA-49-6742       TCGA-49-6745       TCGA-49-6761 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7724       TCGA-55-7725       TCGA-55-7726       TCGA-55-7914 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8203       TCGA-55-8205       TCGA-55-8511       TCGA-55-8621 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-A48X       TCGA-55-A491       TCGA-55-A492       TCGA-55-A4DF 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-64-1677       TCGA-73-4658       TCGA-73-4662       TCGA-73-7498 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7166       TCGA-78-7633       TCGA-78-8660       TCGA-80-5607 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-80-5611       TCGA-91-6836       TCGA-91-7771       TCGA-91-A4BC 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-93-8067       TCGA-95-7043       TCGA-95-7562       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-97-8172 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-97-A4LX       TCGA-97-A4M2       TCGA-97-A4M3       TCGA-97-A4M7 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-J2-8194       TCGA-L9-A443       TCGA-L9-A444       TCGA-MP-A4T8 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4TA       TCGA-MP-A4TC       TCGA-MP-A4TD       TCGA-05-4244 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4249       TCGA-05-4250       TCGA-05-4389       TCGA-05-4390 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4397       TCGA-05-4398       TCGA-05-4415       TCGA-05-4417 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4420       TCGA-05-4422       TCGA-05-4424       TCGA-05-4425 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4426       TCGA-05-4430       TCGA-05-4432       TCGA-05-4433 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-5423       TCGA-05-5425       TCGA-05-5428       TCGA-35-4122 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-35-4123       TCGA-35-5375       TCGA-38-4625       TCGA-38-4626 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-38-4632       TCGA-38-A44F       TCGA-44-2656       TCGA-44-2657 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-3396       TCGA-44-3398       TCGA-44-3918       TCGA-44-4112 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-5643       TCGA-44-5644       TCGA-44-5645       TCGA-44-6144 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-6145       TCGA-44-6148       TCGA-44-6774       TCGA-44-6775 
"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-44-7662       TCGA-44-7667       TCGA-44-7669 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-7672       TCGA-44-8117       TCGA-44-8120       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-A4SS 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-A4SU       TCGA-49-4486       TCGA-49-4487       TCGA-49-4490 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-49-4494       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-49-4514       TCGA-49-6743       TCGA-49-6744 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-49-6767       TCGA-50-5051       TCGA-50-5072       TCGA-50-5931 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-50-5939       TCGA-50-5941       TCGA-50-5942       TCGA-50-6590 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-50-7109       TCGA-50-8457       TCGA-50-8459       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-55-6543 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-6971       TCGA-55-6983       TCGA-55-6985       TCGA-55-7281 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7574       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-55-7913 
"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-55-8208 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8299       TCGA-55-8301       TCGA-55-8302       TCGA-55-8507 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8514       TCGA-55-8614       TCGA-55-8615 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8620       TCGA-55-A48Y       TCGA-55-A48Z       TCGA-55-A490 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-A493       TCGA-55-A494       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-64-1679       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-69-7761       TCGA-69-7763       TCGA-69-7764       TCGA-69-7973 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-69-7974       TCGA-69-7978       TCGA-69-7979       TCGA-69-7980 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-69-8253       TCGA-69-8254       TCGA-69-8255       TCGA-69-A59K 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4666       TCGA-73-4668       TCGA-73-4670 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-73-4675       TCGA-73-4676       TCGA-75-5122       TCGA-75-5125 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-75-5126       TCGA-75-6206       TCGA-75-6207       TCGA-75-6211 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-75-6214       TCGA-75-7027       TCGA-75-7031       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-78-7167       TCGA-78-7220       TCGA-78-7535       TCGA-78-7536 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7537       TCGA-78-7539       TCGA-78-7542       TCGA-78-8640 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-8648       TCGA-78-8655       TCGA-78-8662       TCGA-80-5608 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-83-5908       TCGA-86-6851       TCGA-86-7711       TCGA-86-7714 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-7954       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-86-8281       TCGA-86-8358 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8669       TCGA-86-8673       TCGA-86-8674 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-91-6829       TCGA-91-6830       TCGA-91-6835       TCGA-91-6840 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-91-6849       TCGA-91-8499       TCGA-93-7347       TCGA-93-7348 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-95-7039       TCGA-95-7944 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-95-A4VP       TCGA-97-7546       TCGA-97-7547       TCGA-97-7552 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-97-7553       TCGA-97-7554       TCGA-97-7937       TCGA-97-7938 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-97-7941       TCGA-97-8171       TCGA-97-8174       TCGA-97-8176 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-97-8179       TCGA-97-A4M0       TCGA-97-A4M1       TCGA-97-A4M5 
"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-A4AD       TCGA-J2-A4AG       TCGA-L4-A4E5       TCGA-L4-A4E6 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4SV       TCGA-MP-A4SW       TCGA-MP-A4SY       TCGA-MP-A4T2 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4T4       TCGA-MP-A4T6       TCGA-MP-A4T7       TCGA-MP-A4T9 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4TE       TCGA-MP-A4TF       TCGA-MP-A4TH       TCGA-MP-A4TI 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4TK       TCGA-MP-A5C7       TCGA-NJ-A4YF       TCGA-NJ-A4YG 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-NJ-A4YI       TCGA-NJ-A4YP       TCGA-NJ-A4YQ       TCGA-NJ-A55A 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-NJ-A55O       TCGA-NJ-A55R       TCGA-O1-A52J 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
D31V12, continuous
[1] "Remove cluster labels:" "NUDT11 MUTATED"        
clus
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               1              257 
      TCGA-05-4384       TCGA-05-4396       TCGA-05-4405       TCGA-05-4410 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4427       TCGA-05-5420       TCGA-38-7271       TCGA-44-6147 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-6776       TCGA-44-7661       TCGA-44-7670       TCGA-44-8119 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-1592       TCGA-55-1595       TCGA-55-7724       TCGA-55-7725 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7726       TCGA-55-7914       TCGA-55-8205       TCGA-55-8511 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8621       TCGA-55-A48X       TCGA-55-A491       TCGA-55-A492 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-64-1677       TCGA-73-4662       TCGA-73-7498       TCGA-78-7166 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7633       TCGA-78-8660       TCGA-80-5607       TCGA-91-6836 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-91-A4BC       TCGA-93-8067       TCGA-93-A4JQ       TCGA-95-7043 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-95-7562       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-97-8172       TCGA-97-A4LX       TCGA-97-A4M2 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-97-A4M3       TCGA-97-A4M7       TCGA-J2-8194       TCGA-L9-A443 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-L9-A444       TCGA-MN-A4N1       TCGA-MP-A4T8       TCGA-MP-A4TA 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4TC       TCGA-05-4390       TCGA-05-4415       TCGA-05-4417 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4424       TCGA-05-4433       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-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-44-5644       TCGA-44-5645       TCGA-44-6144 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-6145       TCGA-44-6148       TCGA-44-6774       TCGA-44-6775 
"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-44-7662       TCGA-44-7667       TCGA-44-7669 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-7672       TCGA-44-8117       TCGA-44-8120       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-A4SS 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-A4SU       TCGA-49-4486       TCGA-49-4494       TCGA-49-4505 
"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-55-5899       TCGA-55-6642       TCGA-55-6712       TCGA-55-6971 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7227       TCGA-55-7283       TCGA-55-7570       TCGA-55-7574 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7576       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-55-7913       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-55-8299 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8301       TCGA-55-8302       TCGA-55-8506       TCGA-55-8507 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8514       TCGA-55-8615       TCGA-55-8620 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-A48Y       TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A493 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-A494       TCGA-62-8398       TCGA-64-1681       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-69-7761       TCGA-69-7763       TCGA-69-7764       TCGA-69-7765 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-69-7974       TCGA-69-7979       TCGA-69-8253       TCGA-69-8255 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-69-A59K       TCGA-73-4659       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-75-6214 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-75-7025       TCGA-75-7027       TCGA-75-7031       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-78-7167       TCGA-78-7220       TCGA-78-7535       TCGA-78-7536 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7537       TCGA-78-7539       TCGA-78-7542       TCGA-78-8640 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-8648       TCGA-78-8655       TCGA-78-8662       TCGA-80-5608 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-83-5908       TCGA-86-6851       TCGA-86-7711       TCGA-86-7714 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-7954       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-86-8281       TCGA-86-8358 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8669       TCGA-86-8673       TCGA-86-8674 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-A456       TCGA-91-6829       TCGA-91-6830       TCGA-91-6840 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-91-6849       TCGA-91-8499       TCGA-93-7347       TCGA-93-7348 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-95-7567       TCGA-95-7944 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-95-A4VP       TCGA-97-7546       TCGA-97-7553       TCGA-97-7554 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-97-7941       TCGA-97-8171       TCGA-97-8174       TCGA-97-8176 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-97-8179       TCGA-97-A4M0       TCGA-97-A4M1       TCGA-97-A4M5 
"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-A4AD       TCGA-J2-A4AG       TCGA-L4-A4E5       TCGA-L4-A4E6 
"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-A4T9 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4TE       TCGA-MP-A4TF       TCGA-MP-A4TH       TCGA-MP-A4TI 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4TK       TCGA-MP-A5C7       TCGA-NJ-A4YG       TCGA-NJ-A4YI 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-O1-A52J 
"NUDT11 WILD-TYPE" 
                  vv
clus                R0  R1  R2  RX
  NUDT11 MUTATED     2   0   0   0
  NUDT11 WILD-TYPE 310  12   4  25
D31V13, multiclass
[1] "Remove cluster labels:" "NUDT11 MUTATED"        
clus
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               2              351 
      TCGA-05-4382       TCGA-05-4384       TCGA-05-4396       TCGA-05-4402 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4405       TCGA-05-4410       TCGA-05-4418       TCGA-05-4427 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4434       TCGA-05-5420       TCGA-38-4629       TCGA-38-4630 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-38-4631       TCGA-38-6178       TCGA-38-7271       TCGA-44-2661 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-49-4501       TCGA-49-6742       TCGA-49-6761       TCGA-50-6597 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-1592       TCGA-55-7284       TCGA-55-7724       TCGA-55-7725 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7726       TCGA-55-7914       TCGA-55-8090       TCGA-55-8091 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8203       TCGA-55-8204       TCGA-55-8205       TCGA-55-8207 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8511       TCGA-55-8619       TCGA-55-8621       TCGA-55-A48X 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-A491       TCGA-55-A492       TCGA-55-A4DF       TCGA-64-1677 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-67-6217       TCGA-73-4658       TCGA-73-4662       TCGA-73-7498 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7166       TCGA-78-7633       TCGA-78-8660       TCGA-80-5607 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-80-5611       TCGA-93-8067       TCGA-93-A4JQ       TCGA-95-7562 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-95-7947       TCGA-95-7948       TCGA-95-A4VK       TCGA-95-A4VN 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-97-A4M2       TCGA-97-A4M7       TCGA-L9-A443       TCGA-L9-A444 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MP-A4T8       TCGA-MP-A4TA       TCGA-MP-A4TC 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4TD       TCGA-05-4244       TCGA-05-4249       TCGA-05-4250 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4389       TCGA-05-4390       TCGA-05-4395       TCGA-05-4397 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4398       TCGA-05-4403       TCGA-05-4415       TCGA-05-4417 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4420       TCGA-05-4422       TCGA-05-4424       TCGA-05-4425 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-4426       TCGA-05-4430       TCGA-05-4432       TCGA-05-4433 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-5423       TCGA-05-5425       TCGA-05-5428       TCGA-05-5429 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-05-5715       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-38-4627       TCGA-38-4628 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-38-4632       TCGA-38-A44F       TCGA-44-2657       TCGA-44-2665 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-3396       TCGA-44-3398       TCGA-44-3918       TCGA-44-3919 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-4112       TCGA-44-6144       TCGA-44-6148       TCGA-44-6775 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-A479       TCGA-44-A47A       TCGA-44-A47B       TCGA-44-A47G 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-44-A4SU       TCGA-49-4486       TCGA-49-4487       TCGA-49-4488 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-49-4494       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-49-6744 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-49-6767       TCGA-50-5051       TCGA-50-5055       TCGA-50-5066 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-50-5931       TCGA-50-5942       TCGA-50-5944       TCGA-50-6593 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-50-6673       TCGA-50-8460       TCGA-53-7624       TCGA-53-7626 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-53-A4EZ       TCGA-55-5899       TCGA-55-6642       TCGA-55-6712 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-6970       TCGA-55-6971       TCGA-55-6972       TCGA-55-6980 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-6981       TCGA-55-6983       TCGA-55-6985       TCGA-55-7227 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7281       TCGA-55-7570       TCGA-55-7574       TCGA-55-7576 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7727       TCGA-55-7728       TCGA-55-7815       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-55-7913 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-7994       TCGA-55-7995       TCGA-55-8085       TCGA-55-8087 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8089       TCGA-55-8092       TCGA-55-8094       TCGA-55-8097 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8206       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-55-8512       TCGA-55-8513 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8514       TCGA-55-8614       TCGA-55-8615       TCGA-55-8616 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-8620       TCGA-55-A48Y       TCGA-55-A48Z       TCGA-55-A490 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-55-A493       TCGA-55-A494       TCGA-55-A4DG       TCGA-62-8394 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-62-8395       TCGA-62-8397       TCGA-62-8398       TCGA-62-8399 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-62-8402       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-A46U       TCGA-62-A46V       TCGA-62-A46Y 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-62-A470       TCGA-62-A471       TCGA-62-A472       TCGA-64-1676 
"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-71-6725       TCGA-71-8520       TCGA-73-4659       TCGA-73-4666 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-73-4668       TCGA-73-4670       TCGA-73-4675       TCGA-73-4676 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-73-4677       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-78-7167       TCGA-78-7220       TCGA-78-7535       TCGA-78-7536 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-7537       TCGA-78-7539       TCGA-78-7540       TCGA-78-7542 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-78-8640       TCGA-78-8648       TCGA-78-8655       TCGA-78-8662 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-80-5608       TCGA-83-5908       TCGA-86-6562       TCGA-86-7701 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-7711       TCGA-86-7713       TCGA-86-7714       TCGA-86-7953 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-7954       TCGA-86-7955       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-86-8075 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8280       TCGA-86-8358 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8585       TCGA-86-8668       TCGA-86-8669 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-8671       TCGA-86-8672       TCGA-86-8673       TCGA-86-8674 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-86-A456       TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6828 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-91-6829       TCGA-91-6835       TCGA-91-6840       TCGA-91-A4BD 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-93-7347       TCGA-93-7348       TCGA-93-A4JN       TCGA-93-A4JO 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-93-A4JP       TCGA-95-7944       TCGA-95-8039       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-99-7458       TCGA-99-8025       TCGA-99-8028       TCGA-99-8032 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-99-8033       TCGA-J2-A4AD       TCGA-J2-A4AE       TCGA-J2-A4AG 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-L4-A4E5       TCGA-L4-A4E6       TCGA-MN-A4N4       TCGA-MN-A4N5 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4SV       TCGA-MP-A4SW       TCGA-MP-A4SY       TCGA-MP-A4T2 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4T4       TCGA-MP-A4T6       TCGA-MP-A4T7       TCGA-MP-A4T9 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4TE       TCGA-MP-A4TF       TCGA-MP-A4TH       TCGA-MP-A4TI 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-MP-A4TK       TCGA-MP-A5C7       TCGA-NJ-A4YQ 
"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                        29   374
D31V14, multiclass
                                  clus
vv                                 NUDT11 MUTATED NUDT11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               29
  WHITE                                         4              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"
D31V15, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     0   5
  NUDT11 WILD-TYPE   6 346
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      0    5
  NUDT11 WILD-TYPE    6  346
                        clus
vv                       NUDT11 MUTATED NUDT11 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              5              346
[1] 2 2
[1] FALSE

Clustering(32) Variable = SLAMF9 MUTATION ANALYSIS
D32V1, survival
                  sevent
clus2                0   1
  SLAMF9 MUTATED     7   5
  SLAMF9 WILD-TYPE 291 166
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
              12              457 
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
               5              166 
$`SLAMF9 MUTATED`
TCGA-55-1592 TCGA-L9-A443 TCGA-44-3918 TCGA-50-5930 TCGA-53-7624 TCGA-55-8506 
       23.05         6.35        34.06         9.27        34.29         0.36 
TCGA-55-8507 TCGA-78-7539 TCGA-86-8075 TCGA-86-8358 TCGA-95-7567 TCGA-97-7554 
       13.74        26.01        22.82        21.47        18.67        25.48 

$`SLAMF9 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
       23.80        10.09        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         4.37        46.98        44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       47.41        49.28         8.22        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
        3.91        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
       10.13        36.99        36.79        27.25        30.54        13.94 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       35.21        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       40.73        15.25        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
       70.26        31.30        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
       22.03         3.91        23.15        25.41        15.39        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 
       11.28        34.19        17.65        18.44        19.82        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       29.72        15.19        23.08         5.06        17.79        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       15.65        29.19        22.16        15.42        17.56        15.72 
TCGA-55-8505 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       14.47        20.28        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.62        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        3.25         0.92        15.81        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 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-69-7760 
       18.84        14.04        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41        13.41        13.51        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       19.43         8.42         6.90        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 
        4.31        30.31         9.24         1.25        50.33        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       77.85        43.82        85.15        49.84        36.66       108.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
      100.57       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-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      238.29        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 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        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
        1.08        19.00        41.82        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 
       19.89        42.25        64.60        63.52        61.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59        15.91        18.67         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.57        18.08        35.47        32.48        19.00        14.30 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        47.08         0.49         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
            0.36             0.00 
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
           34.29           238.29 
  SLAMF9 MUTATED SLAMF9 WILD-TYPE 
          22.145           21.440 
[1] "0.4 - 34.3 (22.1)"  "0.0 - 238.3 (21.4)"
[1] "hr=" "1.8"
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      117      130        45        64         68
                  vv
clus               STAGE IIIB STAGE IV
  SLAMF9 MUTATED            0        1
  SLAMF9 WILD-TYPE         11       23
D32V3, multiclass
            clus
vv           SLAMF9 MUTATED SLAMF9 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                4              117
  STAGE IB                2              130
  STAGE IIA               1               45
  STAGE IIB               2               64
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                1               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
  SLAMF9 MUTATED     3   8   1   0
  SLAMF9 WILD-TYPE 153 253  42  18
D32V4, multiclass
    clus
vv   SLAMF9 MUTATED SLAMF9 WILD-TYPE
  T1              3              153
  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 299  88    70
D32V5, multiclass
       clus
vv      SLAMF9 MUTATED SLAMF9 WILD-TYPE
  N0                 9              299
  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 253 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF9 MUTATED      7    5
  SLAMF9 WILD-TYPE  253  216
        clus
vv       SLAMF9 MUTATED SLAMF9 WILD-TYPE
  FEMALE              7              253
  MALE                5              216
[1] 2 2
[1] FALSE
D32V8, binary
                  cls
clus                 0   1
  SLAMF9 MUTATED    10   1
  SLAMF9 WILD-TYPE 374  54
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF9 MUTATED     10    1
  SLAMF9 WILD-TYPE  374   54
     clus
vv    SLAMF9 MUTATED SLAMF9 WILD-TYPE
  NO              10              374
  YES              1               54
[1] 2 2
[1] FALSE
D32V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SLAMF9 MUTATED                            0                                 3
  SLAMF9 WILD-TYPE                         17                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SLAMF9 MUTATED                                                    8
  SLAMF9 WILD-TYPE                                                288
                  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                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                99
  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"
D32V11, continuous
D32V12, continuous
                  vv
clus                R0  R1  R2  RX
  SLAMF9 MUTATED    10   0   0   0
  SLAMF9 WILD-TYPE 302  12   4  25
D32V13, multiclass
    clus
vv   SLAMF9 MUTATED SLAMF9 WILD-TYPE
  R0             10              302
  R1              0               12
  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                        30   366
D32V14, multiclass
                                  clus
vv                                 SLAMF9 MUTATED SLAMF9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               30
  WHITE                                        12              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"
D32V15, binary
                  cls
clus                 0   1
  SLAMF9 MUTATED     1  10
  SLAMF9 WILD-TYPE   5 341
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF9 MUTATED      1   10
  SLAMF9 WILD-TYPE    5  341
                        clus
vv                       SLAMF9 MUTATED SLAMF9 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             10              341
[1] 2 2
[1] FALSE

Clustering(33) Variable = DNMT3A MUTATION ANALYSIS
D33V1, survival
                  sevent
clus2                0   1
  DNMT3A MUTATED    11   8
  DNMT3A WILD-TYPE 287 163
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              19              450 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               8              163 
$`DNMT3A MUTATED`
TCGA-55-8207 TCGA-MP-A4TA TCGA-44-7662 TCGA-50-5931 TCGA-50-6595 TCGA-55-6987 
       32.12        31.23         7.17        14.27         6.21        70.26 
TCGA-55-7913 TCGA-55-8089 TCGA-55-A490 TCGA-64-5774 TCGA-64-5778 TCGA-86-8073 
       18.44        23.08         3.25        87.98        42.90        24.33 
TCGA-86-8672 TCGA-91-6830 TCGA-91-8499 TCGA-97-7547 TCGA-97-8176 TCGA-97-8179 
        0.62         1.97         1.18        64.60        15.39        14.30 
TCGA-NJ-A4YQ 
       47.08 

$`DNMT3A WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       17.98        16.93        19.69        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TC 
       23.80         6.35        10.09        27.19         5.29         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         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-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5933 TCGA-50-5936 
       47.41        49.28         8.22         9.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6673 TCGA-50-7109 
        3.91        25.55        11.05        12.16         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99        36.79        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       35.21        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       40.73        15.25        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       31.30        28.67        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        3.91        23.15        25.41        15.39        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       34.19        17.65        19.82        29.23        29.72        15.19 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42        17.56        15.72        14.47         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A493 
       14.66         1.58        12.33        20.71        21.40         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        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-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 
       56.81        81.80        38.37         2.04        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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41        13.41        13.51        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 
       13.45         4.24        19.43         8.42         6.90        23.38 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
       50.33        66.64        77.85        43.82        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       36.66       108.66       100.57       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        9.57       104.19       238.29        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59       110.50        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.89        35.24        37.74         4.08         4.57         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-86-8673 
       14.60        11.61        13.91        30.84        27.58        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-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       41.36        10.19         2.60        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
        1.15        16.60        14.27        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
       23.61         1.08        19.00        41.82        18.67        12.39 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 
       27.29         2.76        19.89        42.25        63.52        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       25.48        18.54         0.59        15.91        18.67         5.39 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       18.12        16.41        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.57        18.08        35.47        32.48        19.00        14.30 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.13         1.64         0.49         0.43        19.82        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 
           18.44            21.47 
[1] "0.6 - 88.0 (18.4)"  "0.0 - 238.3 (21.5)"
[1] "hr=" "1.2"
D33V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  DNMT3A MUTATED         0        7        7         2         1          2
  DNMT3A WILD-TYPE       4      114      125        44        65         68
                  vv
clus               STAGE IIIB STAGE IV
  DNMT3A MUTATED            0        0
  DNMT3A WILD-TYPE         11       24
D33V3, multiclass
            clus
vv           DNMT3A MUTATED DNMT3A WILD-TYPE
  STAGE I                 0                4
  STAGE IA                7              114
  STAGE IB                7              125
  STAGE IIA               2               44
  STAGE IIB               1               65
  STAGE IIIA              2               68
  STAGE IIIB              0               11
  STAGE IV                0               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
  DNMT3A MUTATED     8   9   2   0
  DNMT3A WILD-TYPE 148 252  41  18
D33V4, multiclass
    clus
vv   DNMT3A MUTATED DNMT3A WILD-TYPE
  T1              8              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    16   2     1
  DNMT3A WILD-TYPE 292  87    71
D33V5, multiclass
       clus
vv      DNMT3A MUTATED DNMT3A WILD-TYPE
  N0                16              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     8  11
  DNMT3A WILD-TYPE 252 210
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      8   11
  DNMT3A WILD-TYPE  252  210
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  FEMALE              8              252
  MALE               11              210
[1] 2 2
[1] FALSE
D33V8, binary
                  cls
clus                 0   1
  DNMT3A MUTATED    17   2
  DNMT3A WILD-TYPE 367  53
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED     17    2
  DNMT3A WILD-TYPE  367   53
     clus
vv    DNMT3A MUTATED DNMT3A WILD-TYPE
  NO              17              367
  YES              2               53
[1] 2 2
[1] FALSE
D33V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DNMT3A MUTATED                            3                                 0
  DNMT3A WILD-TYPE                         14                               102
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DNMT3A MUTATED                                                   13
  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)             13
  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                                       14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               102
  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    11   0   0   1
  DNMT3A WILD-TYPE 301  12   4  24
D33V13, multiclass
    clus
vv   DNMT3A MUTATED DNMT3A WILD-TYPE
  R0             11              301
  R1              0               12
  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                           1    18
  DNMT3A WILD-TYPE                        29   360
D33V14, multiclass
                                  clus
vv                                 DNMT3A MUTATED DNMT3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               29
  WHITE                                        18              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"
D33V15, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     0  19
  DNMT3A WILD-TYPE   6 332
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      0   19
  DNMT3A WILD-TYPE    6  332
                        clus
vv                       DNMT3A MUTATED DNMT3A WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             19              332
[1] 2 2
[1] FALSE

Clustering(34) Variable = CTNNB1 MUTATION ANALYSIS
D34V1, survival
                  sevent
clus2                0   1
  CTNNB1 MUTATED    14   5
  CTNNB1 WILD-TYPE 284 166
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              19              450 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               5              166 
$`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-75-6214 TCGA-78-7153 TCGA-78-7158 TCGA-86-8280 TCGA-97-8171 
       13.41        36.66       119.51         5.88        23.05        18.67 
TCGA-MP-A4SV 
       86.14 

$`CTNNB1 WILD-TYPE`
TCGA-05-4382 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96         9.96         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4390 TCGA-05-4395 
        2.43        10.09        50.07         3.98        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4424 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 
       30.02        26.01        25.02        25.02        24.00         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-38-4632 
        8.68        97.74       120.79        37.71        49.05        44.61 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
        4.37        46.98        44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       19.56        23.15        21.63        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        22.72        19.46         7.17        36.07        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G 
       23.64        12.66         8.55        15.98         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       35.54        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       55.89        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 
      101.72        15.72        60.16        47.41        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        9.27        14.27        78.67         8.45        15.12        48.46 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       60.72        57.53        53.16        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05        12.16         6.21         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.79        27.25        34.29        30.54        13.94        35.21 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       30.58        14.30        80.52         5.62        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       15.25        46.03        53.65         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       31.30        28.67        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        3.91        23.15        25.41        15.39        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 
       34.19        17.65        18.44        19.82        29.23        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       23.08         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       13.74        20.28        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 
       17.62        14.66         1.58        12.33        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        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-64-1679 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-67-6215 TCGA-67-6216 
       51.25        28.47        18.84        14.04         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         4.41        13.51        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       19.43         8.42         6.90        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 
        4.31        30.31         9.24         1.25        50.33        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 
       77.85        43.82        85.15        49.84       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7159 
       21.90        39.95        19.50        38.50        32.09        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
       22.92         9.57       104.19       238.29        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-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-91-8496 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.18        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
       19.00        41.82        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
       18.54         0.59        15.91         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.57        18.08        35.47        32.48        19.00        14.30 
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-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.85         5.49        41.59        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        47.08         0.49         0.43        19.82        59.11 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
            5.88             0.00 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          119.51           238.29 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          21.990           21.455 
[1] "5.9 - 119.5 (22.0)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.6"
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      118      124        44        66         68
                  vv
clus               STAGE IIIB STAGE IV
  CTNNB1 MUTATED            1        2
  CTNNB1 WILD-TYPE         10       22
D34V3, multiclass
            clus
vv           CTNNB1 MUTATED CTNNB1 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              118
  STAGE IB                8              124
  STAGE IIA               2               44
  STAGE IIB               0               66
  STAGE IIIA              2               68
  STAGE IIIB              1               10
  STAGE IV                2               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
  CTNNB1 MUTATED     3  14   1   1
  CTNNB1 WILD-TYPE 153 247  42  17
D34V4, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T1              3              153
  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 293  89    68
D34V5, multiclass
       clus
vv      CTNNB1 MUTATED CTNNB1 WILD-TYPE
  N0                15              293
  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 250 212
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     10    9
  CTNNB1 WILD-TYPE  250  212
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FEMALE             10              250
  MALE                9              212
[1] 2 2
[1] FALSE
D34V8, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    14   1
  CTNNB1 WILD-TYPE 370  54
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     14    1
  CTNNB1 WILD-TYPE  370   54
     clus
vv    CTNNB1 MUTATED CTNNB1 WILD-TYPE
  NO              14              370
  YES              1               54
[1] 2 2
[1] FALSE
D34V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CTNNB1 MUTATED                            2                                 7
  CTNNB1 WILD-TYPE                         15                                95
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CTNNB1 MUTATED                                                    7
  CTNNB1 WILD-TYPE                                                289
                  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                                       15
  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                                    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 298  10   4  24
D34V13, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  R0             14              298
  R1              2               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
  CTNNB1 MUTATED                                  0     1
  CTNNB1 WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CTNNB1 MUTATED                           1    11
  CTNNB1 WILD-TYPE                        29   367
D34V14, multiclass
                                  clus
vv                                 CTNNB1 MUTATED CTNNB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     1               29
  WHITE                                        11              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"
D34V15, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     0  11
  CTNNB1 WILD-TYPE   6 340
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      0   11
  CTNNB1 WILD-TYPE    6  340
                        clus
vv                       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             11              340
[1] 2 2
[1] FALSE

Clustering(35) Variable = PTPRU MUTATION ANALYSIS
D35V1, survival
                 sevent
clus2               0   1
  PTPRU MUTATED    13   5
  PTPRU WILD-TYPE 285 166
  PTPRU MUTATED PTPRU WILD-TYPE 
             18             451 
  PTPRU MUTATED PTPRU WILD-TYPE 
              5             166 
$`PTPRU MUTATED`
TCGA-91-6836 TCGA-05-4397 TCGA-05-4420 TCGA-44-8117 TCGA-49-6744 TCGA-55-6982 
       13.71        24.03        29.98        12.66        55.33        32.71 
TCGA-55-7995 TCGA-55-8506 TCGA-62-A46O TCGA-67-3771 TCGA-69-7978 TCGA-73-4668 
       29.23         0.36        47.80        20.05         4.41        15.35 
TCGA-78-7539 TCGA-86-8279 TCGA-91-6829 TCGA-91-8499 TCGA-J2-A4AD TCGA-MN-A4N4 
       26.01        31.20        41.36         1.18        18.08        38.63 

$`PTPRU WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       10.55        85.32        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 
        0.00        47.05        19.00         2.99        14.96        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        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-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 
       44.61         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-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       36.07        18.87        23.64         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
        9.44        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6767 TCGA-50-5044 
       29.46        29.75        55.89        53.29        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47       101.72        15.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
        8.22         9.27        14.27        78.67         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       48.46        60.72        57.53        53.16        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05        12.16         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99        36.79        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       35.21        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       40.73        15.25        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       45.34        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       31.30        28.67        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        3.91        23.15        25.41        15.39        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
       34.19        17.65        18.44        19.82        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       23.08         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
       22.16        15.42        17.56        15.72        14.47        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       14.66         1.58        12.33        20.71        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       56.81        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-67-4679 
       28.41        51.25        28.47        18.84        14.04        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        5.42         7.56         6.05        13.41        13.51        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 
       13.45         4.24        19.43         8.42         6.90        23.38 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 
       26.30         4.31        30.31         9.24         1.25        50.33 
TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 
       66.64        77.85        43.82        85.15        49.84        36.66 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
      108.66       100.57       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      104.19       238.29        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       53.33        39.35        10.55       232.18        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
      110.50        93.11        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 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        11.61 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-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-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       16.60        14.27        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
        1.08        19.00        41.82        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       25.48        18.54         0.59        15.91        18.67         5.39 
TCGA-97-8175 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-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       36.76         1.45        21.57        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       14.30         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        47.08         0.49         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  PTPRU MUTATED PTPRU WILD-TYPE 
           0.36            0.00 
  PTPRU MUTATED PTPRU WILD-TYPE 
          55.33          238.29 
  PTPRU MUTATED PTPRU WILD-TYPE 
          25.02           21.44 
[1] "0.4 - 55.3 (25.0)"  "0.0 - 238.3 (21.4)"
[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      116      127        43        61         70
                 vv
clus              STAGE IIIB STAGE IV
  PTPRU MUTATED            0        0
  PTPRU WILD-TYPE         11       24
D35V3, multiclass
            clus
vv           PTPRU MUTATED PTPRU WILD-TYPE
  STAGE I                0               4
  STAGE IA               5             116
  STAGE IB               5             127
  STAGE IIA              3              43
  STAGE IIB              5              61
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              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
  PTPRU MUTATED     5  12   1   0
  PTPRU WILD-TYPE 151 249  42  18
D35V4, multiclass
    clus
vv   PTPRU MUTATED PTPRU WILD-TYPE
  T1             5             151
  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 296  83    72
D35V5, multiclass
       clus
vv      PTPRU MUTATED PTPRU WILD-TYPE
  N0               12             296
  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 248 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRU MUTATED     12    6
  PTPRU WILD-TYPE  248  215
        clus
vv       PTPRU MUTATED PTPRU WILD-TYPE
  FEMALE            12             248
  MALE               6             215
[1] 2 2
[1] FALSE
D35V8, binary
                 cls
clus                0   1
  PTPRU MUTATED    14   1
  PTPRU WILD-TYPE 370  54
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRU MUTATED     14    1
  PTPRU WILD-TYPE  370   54
     clus
vv    PTPRU MUTATED PTPRU WILD-TYPE
  NO             14             370
  YES             1              54
[1] 2 2
[1] FALSE
D35V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PTPRU MUTATED                            0                                 5
  PTPRU WILD-TYPE                         17                                97
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PTPRU MUTATED                                                   11
  PTPRU WILD-TYPE                                                285
                 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                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               97
  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                               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 300  12   4  24
D35V13, multiclass
    clus
vv   PTPRU MUTATED PTPRU WILD-TYPE
  R0            12             300
  R1             0              12
  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                        29   364
D35V14, multiclass
                                  clus
vv                                 PTPRU MUTATED PTPRU WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              29
  WHITE                                       14             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"
D35V15, binary
                 cls
clus                0   1
  PTPRU MUTATED     0  13
  PTPRU WILD-TYPE   6 338
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRU MUTATED      0   13
  PTPRU WILD-TYPE    6  338
                        clus
vv                       PTPRU MUTATED PTPRU WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            13             338
[1] 2 2
[1] FALSE

Clustering(36) Variable = PIK3CA MUTATION ANALYSIS
D36V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    13  14
  PIK3CA WILD-TYPE 285 157
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              27              442 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              14              157 
$`PIK3CA MUTATED`
TCGA-44-7670 TCGA-55-7724 TCGA-64-1677 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
       29.00        23.18        20.65         2.86        15.68        15.65 
TCGA-05-4249 TCGA-05-4397 TCGA-44-5643 TCGA-44-5645 TCGA-49-6743 TCGA-50-5044 
       50.07        24.03        33.30        28.01        53.29        20.52 
TCGA-50-6590 TCGA-50-6592 TCGA-55-7574 TCGA-55-7995 TCGA-55-8092 TCGA-73-7499 
       42.35        25.55        32.71        29.23         5.06        50.33 
TCGA-75-6214 TCGA-78-7146 TCGA-78-7153 TCGA-86-7714 TCGA-93-7348 TCGA-97-8177 
       36.66         5.69       119.51        20.55        17.46        16.41 
TCGA-97-8552 TCGA-MP-A4SY TCGA-MP-A4TI 
       20.58        49.35        14.10 

$`PIK3CA WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       18.31        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7725 
       48.62         5.79         7.79         7.99        16.01        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       21.44         6.15        19.66        19.73        17.98        16.93 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       19.69        32.12        18.15        13.68        16.93        22.65 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       20.58        19.59        20.19        13.87        52.60        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 
       39.09         8.48        50.24        10.55        85.32        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-A4VK 
       16.18         1.45         6.12        17.29        16.54        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       18.18        17.92        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 
       24.30        23.80         6.35        10.09        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
       31.23         2.43        10.09         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
        0.00        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         4.37        46.98        44.42        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
       37.15        38.24        34.06        33.73        26.56        28.37 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       23.77        19.56        23.15        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
       61.28        16.44        22.72        19.46         7.17        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       18.87        23.64        12.66         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
        9.44        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-6767 TCGA-50-5045 
       29.46        29.75        55.89        55.33        22.26        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
      101.72        15.72        60.16        47.41        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        9.27        14.27        78.67         8.45        15.12        48.46 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 
       60.72        57.53        53.16         3.91        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 
       34.29        30.54        13.94        35.21        30.58        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       80.52         5.62        42.51        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       53.65         3.88        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26        31.30        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       20.02        27.09        22.03         3.91        23.15        25.41 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 
       15.39        18.64        11.28        34.19        17.65        18.44 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8094 TCGA-55-8096 
       19.82        29.72        15.19        23.08        17.79        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       15.65        29.19        22.16        15.42        17.56        15.72 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
       14.47         0.36        13.74        20.28        17.72        19.96 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
       26.01        17.10        17.62        14.66         1.58        12.33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
       20.71        21.40         3.25         0.92        15.81        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 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-64-1679 
       13.61        39.25        40.96        29.92        56.81        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41        13.41        13.51        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 
       13.45         4.24        19.43         8.42         6.90        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-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 
       66.64        77.85        43.82        85.15        49.84       108.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      100.57       163.10        27.16        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       21.90        39.95        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 
       64.90        22.92         9.57       104.19       238.29        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
       10.55       232.18        39.75        77.59       110.50        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        38.04 
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        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JO 
       14.27         1.18        19.82        22.45        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
       19.00        41.82        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       15.39        14.30        21.60        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 
       18.08        35.47        32.48        19.00        14.30        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-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
        5.49        41.59        29.46        11.05        24.36        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.49         0.43        19.82        59.11 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            2.86             0.00 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          119.51           238.29 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           24.03            21.44 
[1] "2.9 - 119.5 (24.0)" "0.0 - 238.3 (21.4)"
[1] "hr=" "1.4"
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      117      123        43        62         64
                  vv
clus               STAGE IIIB STAGE IV
  PIK3CA MUTATED            1        0
  PIK3CA WILD-TYPE         10       24
D36V3, multiclass
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                 1                3
  STAGE IA                4              117
  STAGE IB                9              123
  STAGE IIA               3               43
  STAGE IIB               4               62
  STAGE IIIA              6               64
  STAGE IIIB              1               10
  STAGE IV                0               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
  PIK3CA MUTATED     8  18   1   1
  PIK3CA WILD-TYPE 148 243  42  17
D36V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              8              148
  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 294  82    66
D36V5, multiclass
       clus
vv      PIK3CA MUTATED PIK3CA WILD-TYPE
  N0                14              294
  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 240 213
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     20    8
  PIK3CA WILD-TYPE  240  213
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             20              240
  MALE                8              213
[1] 2 2
[1] FALSE
D36V8, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    22   4
  PIK3CA WILD-TYPE 362  51
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     22    4
  PIK3CA WILD-TYPE  362   51
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO              22              362
  YES              4               51
[1] 2 2
[1] FALSE
D36V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PIK3CA MUTATED                            0                                 8
  PIK3CA WILD-TYPE                         17                                94
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PIK3CA MUTATED                                                   18
  PIK3CA WILD-TYPE                                                278
                  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                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                94
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              278
  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 295  11   4  24
D36V13, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0             17              295
  R1              1               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
  PIK3CA MUTATED                                  0     0
  PIK3CA WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED                           4    20
  PIK3CA WILD-TYPE                        26   358
D36V14, multiclass
                                  clus
vv                                 PIK3CA MUTATED PIK3CA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     4               26
  WHITE                                        20              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"
D36V15, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     1  20
  PIK3CA WILD-TYPE   5 331
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1   20
  PIK3CA WILD-TYPE    5  331
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             20              331
[1] 2 2
[1] FALSE

Clustering(37) Variable = ZNF608 MUTATION ANALYSIS
D37V1, survival
                  sevent
clus2                0   1
  ZNF608 MUTATED     5   4
  ZNF608 WILD-TYPE 293 167
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               9              460 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               4              167 
$`ZNF608 MUTATED`
TCGA-55-8203 TCGA-95-7562 TCGA-05-4415 TCGA-44-7667 TCGA-55-8299 TCGA-86-8054 
       17.98         2.86         2.99        36.07        15.42        37.74 
TCGA-91-6831 TCGA-91-8497 TCGA-97-A4M5 
       10.19        14.27        20.84 

$`ZNF608 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
       16.54        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        10.09        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       24.03        47.05        19.00        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        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-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 
       44.61         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-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       18.87        23.64        12.66         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
        9.44        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 
       29.46        29.75        55.89        53.29        55.33        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       49.28         8.22         9.27        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
        3.91        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99        36.79        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       13.94        35.21        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
      107.21        70.26        31.30        28.67        20.02        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
       32.71        22.03         3.91        23.15        25.41        15.39 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       18.64        11.28        34.19        17.65        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       29.23        29.72        15.19        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 
       23.64        15.65        29.19        22.16        17.56        15.72 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
       14.47         0.36        13.74        20.28        17.72        19.96 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
       26.01        17.10        17.62        14.66         1.58        12.33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
       20.71        21.40         3.25         0.92        15.81        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 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-64-1679 
       13.61        39.25        40.96        29.92        56.81        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41        13.41        13.51        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 
       13.45         4.24        19.43         8.42         6.90        23.38 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
       50.33        66.64        77.85        43.82        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       36.66       108.66       100.57       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        9.57       104.19       238.29        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59       110.50        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 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        11.61        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-91-6840 TCGA-91-6847 
       10.62        41.36         1.97         2.60        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        7.36         1.15        16.60         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 
       17.46        23.61         1.08        19.00        41.82        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       12.39        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-7458 
       21.60        20.58        21.44        19.76        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE 
       34.85        36.76         1.45        21.57        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       32.48        19.00        14.30        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       41.59        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.49         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 
          15.420           21.585 
[1] "2.9 - 37.7 (15.4)"  "0.0 - 238.3 (21.6)"
[1] "hr=" "2.2"
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      117      131        45        64         70
                  vv
clus               STAGE IIIB STAGE IV
  ZNF608 MUTATED            1        0
  ZNF608 WILD-TYPE         10       24
D37V3, multiclass
            clus
vv           ZNF608 MUTATED ZNF608 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                4              117
  STAGE IB                1              131
  STAGE IIA               1               45
  STAGE IIB               2               64
  STAGE IIIA              0               70
  STAGE IIIB              1               10
  STAGE IV                0               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
  ZNF608 MUTATED     4   3   1   1
  ZNF608 WILD-TYPE 152 258  42  17
D37V4, multiclass
    clus
vv   ZNF608 MUTATED ZNF608 WILD-TYPE
  T1              4              152
  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 302  87    71
D37V5, multiclass
       clus
vv      ZNF608 MUTATED ZNF608 WILD-TYPE
  N0                 6              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"
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 256 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      4    5
  ZNF608 WILD-TYPE  256  216
        clus
vv       ZNF608 MUTATED ZNF608 WILD-TYPE
  FEMALE              4              256
  MALE                5              216
[1] 2 2
[1] FALSE
D37V8, binary
                  cls
clus                 0   1
  ZNF608 MUTATED     9   0
  ZNF608 WILD-TYPE 375  55
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      9    0
  ZNF608 WILD-TYPE  375   55
     clus
vv    ZNF608 MUTATED ZNF608 WILD-TYPE
  NO               9              375
  YES              0               55
[1] 2 2
[1] FALSE
D37V9, continuous
[1] "Remove cluster labels:" "ZNF608 MUTATED"        
clus
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               1              121 
      TCGA-44-6147       TCGA-44-A47F       TCGA-49-6742       TCGA-55-7573 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-55-7725       TCGA-55-7914       TCGA-55-8205       TCGA-55-8511 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-55-8619       TCGA-55-8621       TCGA-55-A491       TCGA-55-A492 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-64-1677       TCGA-73-4662       TCGA-73-7498       TCGA-93-8067 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-35-4122       TCGA-35-4123       TCGA-35-5375 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-44-3396       TCGA-44-3918       TCGA-44-4112       TCGA-44-6144 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-44-6775       TCGA-44-7660       TCGA-49-4486       TCGA-49-4494 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-49-4505       TCGA-49-4506       TCGA-49-4510       TCGA-49-6743 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-49-6744       TCGA-53-7624       TCGA-53-A4EZ       TCGA-55-5899 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7574       TCGA-55-7910       TCGA-55-7913 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-55-7995       TCGA-55-8089       TCGA-55-8096       TCGA-55-8208 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-55-8507       TCGA-55-8508       TCGA-55-8512       TCGA-55-8513 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-55-8620       TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A494 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-62-8394       TCGA-62-8395       TCGA-62-8397       TCGA-62-8398 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O       TCGA-62-A46P 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U       TCGA-62-A46V 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471       TCGA-62-A472 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-64-1681       TCGA-64-5775       TCGA-64-5778       TCGA-69-7974 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-69-8254       TCGA-71-6725       TCGA-71-8520       TCGA-73-4659 
"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-73-7499       TCGA-75-5122       TCGA-83-5908 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-86-6562       TCGA-86-6851       TCGA-86-7701       TCGA-86-7711 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-86-7713       TCGA-86-7714       TCGA-86-7953       TCGA-86-7954 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-86-7955       TCGA-86-8055       TCGA-86-8056       TCGA-86-8073 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-86-8074       TCGA-86-8075       TCGA-86-8076       TCGA-86-8278 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-86-8279       TCGA-86-8280       TCGA-86-8281       TCGA-86-8358 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-86-A456       TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6829 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-91-6849       TCGA-93-7347       TCGA-93-7348       TCGA-93-A4JN 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-93-A4JO       TCGA-95-7567       TCGA-99-7458       TCGA-MN-A4N4 
"ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" "ZNF608 WILD-TYPE" 
      TCGA-MN-A4N5 
"ZNF608 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ZNF608 MUTATED                            1                                 2
  ZNF608 WILD-TYPE                         16                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ZNF608 MUTATED                                                    6
  ZNF608 WILD-TYPE                                                290
                  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                                       16
  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                                    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 308  12   4  24
D37V13, multiclass
    clus
vv   ZNF608 MUTATED ZNF608 WILD-TYPE
  R0              4              308
  R1              0               12
  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                        29   371
D37V14, multiclass
                                  clus
vv                                 ZNF608 MUTATED ZNF608 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               29
  WHITE                                         7              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"
D37V15, binary
                  cls
clus                 0   1
  ZNF608 MUTATED     0   8
  ZNF608 WILD-TYPE   6 343
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      0    8
  ZNF608 WILD-TYPE    6  343
                        clus
vv                       ZNF608 MUTATED ZNF608 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              8              343
[1] 2 2
[1] FALSE

Clustering(38) Variable = STIM1 MUTATION ANALYSIS
D38V1, survival
                 sevent
clus2               0   1
  STIM1 MUTATED     8   1
  STIM1 WILD-TYPE 290 170
  STIM1 MUTATED STIM1 WILD-TYPE 
              9             460 
  STIM1 MUTATED STIM1 WILD-TYPE 
              1             170 
$`STIM1 MUTATED`
TCGA-05-4427 TCGA-95-7043 TCGA-35-4123 TCGA-44-2656 TCGA-55-8510 TCGA-69-7979 
       26.01        16.54         5.98        46.98        17.72        13.41 
TCGA-78-8640 TCGA-86-8673 TCGA-NJ-A4YG 
      232.18        28.34        74.33 

$`STIM1 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        10.09        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 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-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       44.61         4.37        44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       23.77        19.56        23.15        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
       61.28        16.44        22.72        19.46         7.17        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       18.87        23.64        12.66         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
        9.44        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 
       29.46        29.75        55.89        53.29        55.33        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       49.28         8.22         9.27        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
        3.91        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99        36.79        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       13.94        35.21        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
      107.21        70.26        31.30        28.67        20.02        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
       32.71        22.03         3.91        23.15        25.41        15.39 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       18.64        11.28        34.19        17.65        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       29.23        29.72        15.19        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 
       15.72        14.47         0.36        13.74        20.28        19.96 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
       26.01        17.10        17.62        14.66         1.58        12.33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
       20.71        21.40         3.25         0.92        15.81        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 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-64-1679 
       13.61        39.25        40.96        29.92        56.81        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05         4.41        13.51        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 
        4.24        19.43         8.42         6.90        23.38        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-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 
       66.64        77.85        43.82        85.15        49.84        36.66 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
      108.66       100.57       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      104.19       238.29        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 
       53.33        26.01        39.35        10.55        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
      110.50        93.11        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 
       11.61        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-91-6840 TCGA-91-6847 TCGA-91-6848 
        1.97        10.19         2.60        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 
       17.46        23.61         1.08        19.00        41.82        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       12.39        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       21.60        20.58        21.44        19.76        20.84        18.67 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
       24.56        34.85        36.76         1.45        21.57        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 
       35.47        32.48        19.00        14.30        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        5.49        41.59        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       19.13        73.91        71.05         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.49         0.43        19.82        59.11 

  STIM1 MUTATED STIM1 WILD-TYPE 
           5.98            0.00 
  STIM1 MUTATED STIM1 WILD-TYPE 
         232.18          238.29 
  STIM1 MUTATED STIM1 WILD-TYPE 
         26.010          21.455 
[1] "6.0 - 232.2 (26.0)" "0.0 - 238.3 (21.5)"
[1] "hr=" "4.9"
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      119      127        45        65         70
                 vv
clus              STAGE IIIB STAGE IV
  STIM1 MUTATED            0        0
  STIM1 WILD-TYPE         11       24
D38V3, multiclass
            clus
vv           STIM1 MUTATED STIM1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             119
  STAGE IB               5             127
  STAGE IIA              1              45
  STAGE IIB              1              65
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              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
  STIM1 MUTATED     3   6   0   0
  STIM1 WILD-TYPE 153 255  43  18
D38V4, multiclass
    clus
vv   STIM1 MUTATED STIM1 WILD-TYPE
  T1             3             153
  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 301  87    72
D38V5, multiclass
       clus
vv      STIM1 MUTATED STIM1 WILD-TYPE
  N0                7             301
  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 256 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STIM1 MUTATED      4    5
  STIM1 WILD-TYPE  256  216
        clus
vv       STIM1 MUTATED STIM1 WILD-TYPE
  FEMALE             4             256
  MALE               5             216
[1] 2 2
[1] FALSE
D38V8, binary
                 cls
clus                0   1
  STIM1 MUTATED     8   0
  STIM1 WILD-TYPE 376  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STIM1 MUTATED      8    0
  STIM1 WILD-TYPE  376   55
     clus
vv    STIM1 MUTATED STIM1 WILD-TYPE
  NO              8             376
  YES             0              55
[1] 2 2
[1] FALSE
D38V9, continuous
[1] "Remove cluster labels:" "STIM1 MUTATED"         
clus
  STIM1 MUTATED STIM1 WILD-TYPE 
              1             121 
     TCGA-44-6147      TCGA-44-A47F      TCGA-49-6742      TCGA-55-7573 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7914      TCGA-55-8205      TCGA-55-8511 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8621      TCGA-55-A491      TCGA-55-A492 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-64-1677      TCGA-73-4662      TCGA-73-7498      TCGA-93-8067 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-35-4122      TCGA-35-5375      TCGA-44-3396 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-44-3918      TCGA-44-4112      TCGA-44-6144      TCGA-44-6775 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-44-7660      TCGA-49-4486      TCGA-49-4494      TCGA-49-4505 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-49-4506      TCGA-49-4510      TCGA-49-6743      TCGA-49-6744 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-53-7624      TCGA-53-A4EZ      TCGA-55-5899      TCGA-55-7283 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-55-7574      TCGA-55-7910      TCGA-55-7913      TCGA-55-7995 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-55-8089      TCGA-55-8096      TCGA-55-8208      TCGA-55-8507 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-55-8508      TCGA-55-8512      TCGA-55-8513      TCGA-55-8620 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A494      TCGA-62-8394 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-62-8395      TCGA-62-8397      TCGA-62-8398      TCGA-62-8399 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-62-8402      TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-62-A46S      TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-62-A470      TCGA-62-A471      TCGA-62-A472      TCGA-64-1681 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-64-5775      TCGA-64-5778      TCGA-69-7974      TCGA-69-8254 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-71-6725      TCGA-71-8520      TCGA-73-4659      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-73-7499      TCGA-75-5122      TCGA-83-5908      TCGA-86-6562 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-86-6851      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7953      TCGA-86-7954      TCGA-86-7955 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-86-8054      TCGA-86-8055      TCGA-86-8056      TCGA-86-8073 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8075      TCGA-86-8076      TCGA-86-8278 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8280      TCGA-86-8281      TCGA-86-8358 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-86-A456      TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6829 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-91-6849      TCGA-93-7347      TCGA-93-7348      TCGA-93-A4JN 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-93-A4JO      TCGA-95-7567      TCGA-99-7458      TCGA-MN-A4N4 
"STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" "STIM1 WILD-TYPE" 
     TCGA-MN-A4N5 
"STIM1 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  STIM1 MUTATED                            1                                 2
  STIM1 WILD-TYPE                         16                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  STIM1 MUTATED                                                    5
  STIM1 WILD-TYPE                                                291
                 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                                      16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             291
  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 307  12   4  25
D38V13, multiclass
    clus
vv   STIM1 MUTATED STIM1 WILD-TYPE
  R0             5             307
  R1             0              12
  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                        30   371
D38V14, multiclass
                                  clus
vv                                 STIM1 MUTATED STIM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              30
  WHITE                                        7             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"
D38V15, binary
                 cls
clus                0   1
  STIM1 MUTATED     0   6
  STIM1 WILD-TYPE   6 345
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STIM1 MUTATED      0    6
  STIM1 WILD-TYPE    6  345
                        clus
vv                       STIM1 MUTATED STIM1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             345
[1] 2 2
[1] FALSE

Clustering(39) Variable = EMG1 MUTATION ANALYSIS
D39V1, survival
                sevent
clus2              0   1
  EMG1 MUTATED     3   1
  EMG1 WILD-TYPE 295 170
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            465 
  EMG1 MUTATED EMG1 WILD-TYPE 
             1            170 
$`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-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       17.29        16.54         2.86        15.68        15.65        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       18.18        17.92        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 
       24.30        23.80         6.35        10.09        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 
       31.23         2.43        10.09        50.07         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       37.02         0.00        24.03        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        24.00         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-38-4632 TCGA-38-A44F TCGA-44-2657 
      120.79        37.71        49.05        44.61         4.37        44.42 
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-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       55.33        22.26        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       53.16        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 
       34.29        30.54        13.94        35.21        30.58        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       80.52         5.62        42.51        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       53.65         3.88        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26        31.30        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       20.02        27.09        32.71        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       25.41        15.39        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.44        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42        17.56        15.72        14.47         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       14.66         1.58        12.33        20.71        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       29.92        56.81        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-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
       14.73         5.72         4.64         6.64         6.12        22.68 
TCGA-69-7764 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        13.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       13.51        14.01         4.24        19.43         8.42         6.90 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       23.38        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
        1.25        50.33        66.64        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       49.84        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
       22.92         9.57       104.19       238.29        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
        1.08        19.00        41.82        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       25.48        18.54         0.59        15.91        18.67         5.39 
TCGA-97-8175 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-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       36.76         1.45        21.57        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       19.00        14.30        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       49.35        37.35        86.04        58.85         5.49        41.59 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        24.36        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        74.33         0.13         1.64        47.08         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-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         21.470 
[1] "13.4 - 47.0 (23.9)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.4"
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      120      130        46        65         70
                vv
clus             STAGE IIIB STAGE IV
  EMG1 MUTATED            0        0
  EMG1 WILD-TYPE         11       24
D39V3, multiclass
            clus
vv           EMG1 MUTATED EMG1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            120
  STAGE IB              2            130
  STAGE IIA             0             46
  STAGE IIB             1             65
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             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
  EMG1 MUTATED     1   4   0   0
  EMG1 WILD-TYPE 155 257  43  18
D39V4, multiclass
    clus
vv   EMG1 MUTATED EMG1 WILD-TYPE
  T1            1            155
  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 305  88    72
D39V5, multiclass
       clus
vv      EMG1 MUTATED EMG1 WILD-TYPE
  N0               3            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"
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 257 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      3    2
  EMG1 WILD-TYPE  257  219
        clus
vv       EMG1 MUTATED EMG1 WILD-TYPE
  FEMALE            3            257
  MALE              2            219
[1] 2 2
[1] FALSE
D39V8, binary
                cls
clus               0   1
  EMG1 MUTATED     4   0
  EMG1 WILD-TYPE 380  55
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      4    0
  EMG1 WILD-TYPE  380   55
     clus
vv    EMG1 MUTATED EMG1 WILD-TYPE
  NO             4            380
  YES            0             55
[1] 2 2
[1] FALSE
D39V9, continuous
[1] "Remove cluster labels:" "EMG1 MUTATED"          
clus
  EMG1 MUTATED EMG1 WILD-TYPE 
             1            121 
    TCGA-44-6147     TCGA-44-A47F     TCGA-49-6742     TCGA-55-7573 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-7725     TCGA-55-7914     TCGA-55-8205     TCGA-55-8511 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8621     TCGA-55-A491     TCGA-55-A492 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-64-1677     TCGA-73-4662     TCGA-73-7498     TCGA-93-8067 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-35-4122     TCGA-35-4123     TCGA-35-5375 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-44-3396     TCGA-44-3918     TCGA-44-4112     TCGA-44-6144 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-44-6775     TCGA-44-7660     TCGA-49-4486     TCGA-49-4494 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-49-4505     TCGA-49-4506     TCGA-49-4510     TCGA-49-6743 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-49-6744     TCGA-53-7624     TCGA-53-A4EZ     TCGA-55-5899 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7574     TCGA-55-7910     TCGA-55-7913 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-7995     TCGA-55-8089     TCGA-55-8096     TCGA-55-8208 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-8507     TCGA-55-8508     TCGA-55-8512     TCGA-55-8513 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-8620     TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A494 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-62-8394     TCGA-62-8395     TCGA-62-8397     TCGA-62-8398 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O     TCGA-62-A46P 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U     TCGA-62-A46V 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471     TCGA-62-A472 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-64-1681     TCGA-64-5775     TCGA-64-5778     TCGA-69-7974 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-71-6725     TCGA-71-8520     TCGA-73-4659     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-73-7499     TCGA-75-5122     TCGA-83-5908     TCGA-86-6562 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-6851     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7953     TCGA-86-7954     TCGA-86-7955 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-8054     TCGA-86-8055     TCGA-86-8056     TCGA-86-8073 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-8074     TCGA-86-8075     TCGA-86-8076     TCGA-86-8278 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-8279     TCGA-86-8280     TCGA-86-8281     TCGA-86-8358 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6829 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-91-6849     TCGA-93-7347     TCGA-93-7348     TCGA-93-A4JN 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-93-A4JO     TCGA-95-7567     TCGA-99-7458     TCGA-MN-A4N4 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-MN-A4N5 
"EMG1 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  EMG1 MUTATED                            0                                 1
  EMG1 WILD-TYPE                         17                               101
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  EMG1 MUTATED                                                    4
  EMG1 WILD-TYPE                                                292
                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                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             101
  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"
D39V11, continuous
D39V12, continuous
[1] "Remove cluster labels:" "EMG1 MUTATED"          
clus
  EMG1 MUTATED EMG1 WILD-TYPE 
             2            256 
    TCGA-05-4384     TCGA-05-4396     TCGA-05-4405     TCGA-05-4410 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-05-4427     TCGA-05-5420     TCGA-38-7271     TCGA-44-6147 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-44-6776     TCGA-44-7661     TCGA-44-7670     TCGA-44-8119 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-44-A47F     TCGA-55-1592     TCGA-55-1595     TCGA-55-7724 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-7725     TCGA-55-7726     TCGA-55-7914     TCGA-55-8205 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-8511     TCGA-55-8621     TCGA-55-A48X     TCGA-55-A491 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-A492     TCGA-64-1677     TCGA-73-4662     TCGA-73-7498 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-78-7166     TCGA-78-7633     TCGA-78-8660     TCGA-91-6836 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-91-A4BC     TCGA-93-8067     TCGA-93-A4JQ     TCGA-95-7043 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-95-7562     TCGA-95-7947     TCGA-95-7948     TCGA-95-A4VK 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-95-A4VN     TCGA-97-8172     TCGA-97-A4LX     TCGA-97-A4M2 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-97-A4M3     TCGA-97-A4M7     TCGA-J2-8194     TCGA-L9-A443 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MP-A4T8     TCGA-MP-A4TA 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-MP-A4TC     TCGA-05-4390     TCGA-05-4415     TCGA-05-4417 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-05-4424     TCGA-05-4433     TCGA-05-5423     TCGA-05-5425 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-05-5428     TCGA-35-4122     TCGA-35-4123     TCGA-35-5375 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-38-4625     TCGA-38-4626     TCGA-38-A44F     TCGA-44-2657 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-44-3396     TCGA-44-3398     TCGA-44-3918     TCGA-44-4112 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-44-5644     TCGA-44-5645     TCGA-44-6144     TCGA-44-6145 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-44-6148     TCGA-44-6774     TCGA-44-6775     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-44-7662     TCGA-44-7667     TCGA-44-7669     TCGA-44-7672 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-44-8117     TCGA-44-8120     TCGA-44-A479     TCGA-44-A47A 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-44-A47B     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-55-5899 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-6642     TCGA-55-6712     TCGA-55-6971     TCGA-55-7227 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7570     TCGA-55-7574     TCGA-55-7576 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-7728     TCGA-55-7907     TCGA-55-7910     TCGA-55-7911 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-7913     TCGA-55-8089     TCGA-55-8092     TCGA-55-8094 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-8096     TCGA-55-8097     TCGA-55-8299     TCGA-55-8301 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-8302     TCGA-55-8506     TCGA-55-8507     TCGA-55-8512 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-8514     TCGA-55-8615     TCGA-55-8620     TCGA-55-A48Y 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A493     TCGA-55-A494 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-62-8398     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-73-4666     TCGA-73-4668     TCGA-73-4670 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-73-4675     TCGA-73-4676     TCGA-75-6214     TCGA-75-7025 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-75-7027     TCGA-75-7031     TCGA-78-7145     TCGA-78-7146 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-78-7147     TCGA-78-7148     TCGA-78-7149     TCGA-78-7150 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-78-7152     TCGA-78-7153     TCGA-78-7154     TCGA-78-7155 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-78-7156     TCGA-78-7158     TCGA-78-7159     TCGA-78-7160 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-78-7161     TCGA-78-7162     TCGA-78-7163     TCGA-78-7167 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-78-7220     TCGA-78-7535     TCGA-78-7536     TCGA-78-7537 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-78-7539     TCGA-78-7542     TCGA-78-8640     TCGA-78-8648 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-78-8655     TCGA-78-8662     TCGA-80-5608     TCGA-83-5908 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-6851     TCGA-86-7711     TCGA-86-7714     TCGA-86-7954 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-8054     TCGA-86-8055     TCGA-86-8056     TCGA-86-8073 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-8074     TCGA-86-8281     TCGA-86-8358     TCGA-86-8359 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-86-8669     TCGA-86-8673     TCGA-86-8674     TCGA-86-A456 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-91-6829     TCGA-91-6830     TCGA-91-6840     TCGA-91-6849 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-91-8499     TCGA-93-7347     TCGA-93-7348     TCGA-93-A4JN 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-93-A4JO     TCGA-95-7567     TCGA-95-7944     TCGA-95-A4VP 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-97-7546     TCGA-97-7553     TCGA-97-7554     TCGA-97-7941 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-97-8171     TCGA-97-8174     TCGA-97-8176     TCGA-97-8179 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-97-A4M0     TCGA-97-A4M1     TCGA-97-A4M5     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-A4AD 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6     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-A4T9     TCGA-MP-A4TE 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-MP-A4TF     TCGA-MP-A4TH     TCGA-MP-A4TI     TCGA-MP-A4TK 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-MP-A5C7     TCGA-NJ-A4YG     TCGA-NJ-A4YI     TCGA-O1-A52J 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
                vv
clus              R0  R1  R2  RX
  EMG1 MUTATED     3   0   0   0
  EMG1 WILD-TYPE 309  12   4  25
D39V13, multiclass
    clus
vv   EMG1 MUTATED EMG1 WILD-TYPE
  R0            3            309
  R1            0             12
  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                        30   374
D39V14, multiclass
                                  clus
vv                                 EMG1 MUTATED EMG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             30
  WHITE                                       4            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"
D39V15, binary
                cls
clus               0   1
  EMG1 MUTATED     0   4
  EMG1 WILD-TYPE   6 347
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      0    4
  EMG1 WILD-TYPE    6  347
                        clus
vv                       EMG1 MUTATED EMG1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            4            347
[1] 2 2
[1] FALSE

Clustering(40) Variable = PHKA1 MUTATION ANALYSIS
D40V1, survival
                 sevent
clus2               0   1
  PHKA1 MUTATED     9   3
  PHKA1 WILD-TYPE 289 168
  PHKA1 MUTATED PHKA1 WILD-TYPE 
             12             457 
  PHKA1 MUTATED PHKA1 WILD-TYPE 
              3             168 
$`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-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       17.29        16.54         2.86        15.68        15.65        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       18.18        17.92        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 
       24.30        23.80         6.35        10.09        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 
       31.23         2.43        10.09        50.07         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       37.02         0.00        24.03        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        24.00         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-38-4632 TCGA-38-A44F TCGA-44-2656 
      120.79        37.71        49.05        44.61         4.37        46.98 
TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        23.18        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       22.72        19.46         7.17        36.07        18.87        23.64 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
        8.55        15.98        15.32         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6743 TCGA-49-6744 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       53.29        55.33        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       53.16        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       34.29        13.94        35.21        30.58        14.30        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
        5.62        42.51        40.73        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
      107.21        70.26        31.30        28.67        20.02        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
       32.71        22.03         3.91        23.15        25.41        15.39 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       18.64        11.28        34.19        17.65        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       29.23        29.72        15.19        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
       15.72        14.47        13.74        20.28        17.72        19.96 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
       26.01        17.10        17.62        14.66         1.58        12.33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
       20.71        21.40         3.25         0.92        15.81        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 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-64-1681 TCGA-64-5774 
       39.25        40.96        29.92        56.81        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 
        2.04        42.90        28.41        51.25        28.47        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
       14.04        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
       13.41        13.51        14.01        13.45         4.24        19.43 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        8.42         6.90        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       30.31         9.24         1.25        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 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-78-7162 TCGA-78-7163 TCGA-78-7167 
        5.88        64.90        22.92       104.19       238.29        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
       10.55       232.18        39.75        77.59       110.50        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 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-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       20.55        32.78        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 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        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.18        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
       19.00        41.82        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       15.39        16.41        14.30        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       19.76        20.84        18.67        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
        1.45        21.57        18.08        35.47        32.48        14.30 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        47.08         0.49         0.43        19.82 
TCGA-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           21.57 
[1] "0.4 - 88.6 (20.0)"  "0.0 - 238.3 (21.6)"
[1] "hr=" "1.4"
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      120      129        45        63         67
                 vv
clus              STAGE IIIB STAGE IV
  PHKA1 MUTATED            0        0
  PHKA1 WILD-TYPE         11       24
D40V3, multiclass
            clus
vv           PHKA1 MUTATED PHKA1 WILD-TYPE
  STAGE I                1               3
  STAGE IA               1             120
  STAGE IB               3             129
  STAGE IIA              1              45
  STAGE IIB              3              63
  STAGE IIIA             3              67
  STAGE IIIB             0              11
  STAGE IV               0              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
  PHKA1 MUTATED     4   5   3   0
  PHKA1 WILD-TYPE 152 256  40  18
D40V4, multiclass
    clus
vv   PHKA1 MUTATED PHKA1 WILD-TYPE
  T1             4             152
  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 300  88    69
D40V5, multiclass
       clus
vv      PHKA1 MUTATED PHKA1 WILD-TYPE
  N0                8             300
  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 250 219
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKA1 MUTATED     10    2
  PHKA1 WILD-TYPE  250  219
        clus
vv       PHKA1 MUTATED PHKA1 WILD-TYPE
  FEMALE            10             250
  MALE               2             219
[1] 2 2
[1] FALSE
D40V8, binary
                 cls
clus                0   1
  PHKA1 MUTATED     8   1
  PHKA1 WILD-TYPE 376  54
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKA1 MUTATED      8    1
  PHKA1 WILD-TYPE  376   54
     clus
vv    PHKA1 MUTATED PHKA1 WILD-TYPE
  NO              8             376
  YES             1              54
[1] 2 2
[1] FALSE
D40V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PHKA1 MUTATED                            0                                 1
  PHKA1 WILD-TYPE                         17                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PHKA1 MUTATED                                                    8
  PHKA1 WILD-TYPE                                                288
                 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                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  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"
D40V11, continuous
D40V12, continuous
                 vv
clus               R0  R1  R2  RX
  PHKA1 MUTATED     9   2   0   0
  PHKA1 WILD-TYPE 303  10   4  25
D40V13, multiclass
    clus
vv   PHKA1 MUTATED PHKA1 WILD-TYPE
  R0             9             303
  R1             2              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
  PHKA1 MUTATED                                  0     0
  PHKA1 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PHKA1 MUTATED                           1    11
  PHKA1 WILD-TYPE                        29   367
D40V14, multiclass
                                  clus
vv                                 PHKA1 MUTATED PHKA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              29
  WHITE                                       11             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"
D40V15, binary
                 cls
clus                0   1
  PHKA1 MUTATED     0   9
  PHKA1 WILD-TYPE   6 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHKA1 MUTATED      0    9
  PHKA1 WILD-TYPE    6  342
                        clus
vv                       PHKA1 MUTATED PHKA1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             9             342
[1] 2 2
[1] FALSE

Clustering(41) Variable = PAK1 MUTATION ANALYSIS
D41V1, survival
                sevent
clus2              0   1
  PAK1 MUTATED     4   4
  PAK1 WILD-TYPE 294 167
  PAK1 MUTATED PAK1 WILD-TYPE 
             8            461 
  PAK1 MUTATED PAK1 WILD-TYPE 
             4            167 
$`PAK1 MUTATED`
TCGA-95-7562 TCGA-49-6744 TCGA-78-7150 TCGA-78-7156 TCGA-86-7713 TCGA-86-8672 
        2.86        55.33        21.90        32.09        38.04         0.62 
TCGA-91-6830 TCGA-97-7553 
        1.97        61.48 

$`PAK1 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       17.29        16.54        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       29.98        12.00        30.02        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       25.02        24.00         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       37.71        49.05        44.61         4.37        46.98        44.42 
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-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       19.46         7.17        36.07        18.87        23.64        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
        8.55        15.98        15.32         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6743 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       53.29        22.26        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       53.16        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 
       34.29        30.54        13.94        35.21        30.58        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       80.52         5.62        42.51        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       53.65         3.88        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26        31.30        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       20.02        27.09        32.71        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       25.41        15.39        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.44        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42        17.56        15.72        14.47         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       14.66         1.58        12.33        20.71        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       29.92        56.81        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-69-7760 TCGA-69-7761 
       14.04        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
       13.41        13.51        14.01        13.45         4.24        19.43 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        8.42         6.90        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       30.31         9.24         1.25        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 
       39.95       119.51        19.50        38.50         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
       22.92         9.57       104.19       238.29        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 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        11.61        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-91-6840 TCGA-91-6847 
       10.62        41.36        10.19         2.60        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
        7.36         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       22.45        17.46        23.61         1.08        19.00        41.82 
TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 
       18.67        12.39        27.29         2.76        19.89        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       64.60        63.52        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       21.60        20.58        21.44        19.76        20.84        18.67 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
       24.56        34.85        36.76         1.45        21.57        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 
       35.47        32.48        19.00        14.30        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        5.49        41.59        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       47.08         0.49         0.43        19.82        59.11 

  PAK1 MUTATED PAK1 WILD-TYPE 
          0.62           0.00 
  PAK1 MUTATED PAK1 WILD-TYPE 
         61.48         238.29 
  PAK1 MUTATED PAK1 WILD-TYPE 
        26.995         21.440 
[1] "0.6 - 61.5 (27.0)"  "0.0 - 238.3 (21.4)"
[1] "hr=" "1.3"
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      119      132        42        64         70
                vv
clus             STAGE IIIB STAGE IV
  PAK1 MUTATED            0        1
  PAK1 WILD-TYPE         11       23
D41V3, multiclass
            clus
vv           PAK1 MUTATED PAK1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              2            119
  STAGE IB              0            132
  STAGE IIA             4             42
  STAGE IIB             2             64
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              1             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
  PAK1 MUTATED     3   4   1   1
  PAK1 WILD-TYPE 153 257  42  17
D41V4, multiclass
    clus
vv   PAK1 MUTATED PAK1 WILD-TYPE
  T1            3            153
  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 305  84    72
D41V5, multiclass
       clus
vv      PAK1 MUTATED PAK1 WILD-TYPE
  N0               3            305
  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 257 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      3    6
  PAK1 WILD-TYPE  257  215
        clus
vv       PAK1 MUTATED PAK1 WILD-TYPE
  FEMALE            3            257
  MALE              6            215
[1] 2 2
[1] FALSE
D41V8, binary
                cls
clus               0   1
  PAK1 MUTATED     8   0
  PAK1 WILD-TYPE 376  55
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      8    0
  PAK1 WILD-TYPE  376   55
     clus
vv    PAK1 MUTATED PAK1 WILD-TYPE
  NO             8            376
  YES            0             55
[1] 2 2
[1] FALSE
D41V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PAK1 MUTATED                            0                                 2
  PAK1 WILD-TYPE                         17                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PAK1 MUTATED                                                    6
  PAK1 WILD-TYPE                                                290
                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                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             100
  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"
D41V11, continuous
D41V12, continuous
                vv
clus              R0  R1  R2  RX
  PAK1 MUTATED     5   0   0   1
  PAK1 WILD-TYPE 307  12   4  24
D41V13, multiclass
    clus
vv   PAK1 MUTATED PAK1 WILD-TYPE
  R0            5            307
  R1            0             12
  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                        29   370
D41V14, multiclass
                                  clus
vv                                 PAK1 MUTATED PAK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             29
  WHITE                                       8            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"
D41V15, binary
                cls
clus               0   1
  PAK1 MUTATED     0   6
  PAK1 WILD-TYPE   6 345
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      0    6
  PAK1 WILD-TYPE    6  345
                        clus
vv                       PAK1 MUTATED PAK1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            6            345
[1] 2 2
[1] FALSE

Clustering(42) Variable = NRAS MUTATION ANALYSIS
D42V1, survival
                sevent
clus2              0   1
  NRAS MUTATED     2   1
  NRAS WILD-TYPE 296 170
  NRAS MUTATED NRAS WILD-TYPE 
             3            466 
  NRAS MUTATED NRAS WILD-TYPE 
             1            170 
$`NRAS MUTATED`
TCGA-35-4123 TCGA-38-4632 TCGA-69-7979 
        5.98        44.61        13.41 

$`NRAS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       17.29        16.54         2.86        15.68        15.65        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       18.18        17.92        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 
       24.30        23.80         6.35        10.09        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 
       31.23         2.43        10.09        50.07         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       37.02         0.00        24.03        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        24.00         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-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       37.71        49.05         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-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       55.33        22.26        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       53.16        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 
       34.29        30.54        13.94        35.21        30.58        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       80.52         5.62        42.51        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       53.65         3.88        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26        31.30        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       20.02        27.09        32.71        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       25.41        15.39        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.44        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42        17.56        15.72        14.47         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       14.66         1.58        12.33        20.71        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       29.92        56.81        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-69-7760 TCGA-69-7761 
       14.04        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       13.51        14.01        13.45         4.24        19.43         8.42 
TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        6.90        23.38        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
        9.24         1.25        50.33        66.64        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       85.15        49.84        36.66       108.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 
       64.90        22.92         9.57       104.19       238.29        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
       10.55       232.18        39.75        77.59       110.50        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 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        11.61        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        12.23        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
       23.61         1.08        19.00        41.82        18.67        12.39 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       27.29         2.76        19.89        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       61.48        25.48        18.54         0.59        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       20.58        21.44        19.76        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE 
       34.85        36.76         1.45        21.57        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       32.48        19.00        14.30        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       41.59        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.49         0.43        19.82        59.11 

  NRAS MUTATED NRAS WILD-TYPE 
          5.98           0.00 
  NRAS MUTATED NRAS WILD-TYPE 
         44.61         238.29 
  NRAS MUTATED NRAS WILD-TYPE 
         13.41          21.47 
[1] "6.0 - 44.6 (13.4)"  "0.0 - 238.3 (21.5)"
[1] "hr=" "1.2"
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      120      131        46        66         70
                vv
clus             STAGE IIIB STAGE IV
  NRAS MUTATED            0        1
  NRAS WILD-TYPE         11       23
D42V3, multiclass
            clus
vv           NRAS MUTATED NRAS WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            120
  STAGE IB              1            131
  STAGE IIA             0             46
  STAGE IIB             0             66
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              1             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
  NRAS MUTATED     1   2   0   0
  NRAS WILD-TYPE 155 259  43  18
D42V4, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  T1            1            155
  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 306  88    72
D42V5, multiclass
       clus
vv      NRAS MUTATED NRAS WILD-TYPE
  N0               2            306
  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 259 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      1    2
  NRAS WILD-TYPE  259  219
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE            1            259
  MALE              2            219
[1] 2 2
[1] FALSE
D42V8, binary
                cls
clus               0   1
  NRAS MUTATED     2   0
  NRAS WILD-TYPE 382  55
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      2    0
  NRAS WILD-TYPE  382   55
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO             2            382
  YES            0             55
[1] 2 2
[1] FALSE
D42V9, continuous
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             1            121 
    TCGA-44-6147     TCGA-44-A47F     TCGA-49-6742     TCGA-55-7573 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7725     TCGA-55-7914     TCGA-55-8205     TCGA-55-8511 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8621     TCGA-55-A491     TCGA-55-A492 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-64-1677     TCGA-73-4662     TCGA-73-7498     TCGA-93-8067 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-35-4122     TCGA-35-5375     TCGA-44-3396 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-3918     TCGA-44-4112     TCGA-44-6144     TCGA-44-6775 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-7660     TCGA-49-4486     TCGA-49-4494     TCGA-49-4505 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-49-4506     TCGA-49-4510     TCGA-49-6743     TCGA-49-6744 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-53-7624     TCGA-53-A4EZ     TCGA-55-5899     TCGA-55-7283 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7574     TCGA-55-7910     TCGA-55-7913     TCGA-55-7995 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8089     TCGA-55-8096     TCGA-55-8208     TCGA-55-8507 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8508     TCGA-55-8512     TCGA-55-8513     TCGA-55-8620 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A494     TCGA-62-8394 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-62-8395     TCGA-62-8397     TCGA-62-8398     TCGA-62-8399 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-62-8402     TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-62-A46S     TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-62-A470     TCGA-62-A471     TCGA-62-A472     TCGA-64-1681 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-64-5775     TCGA-64-5778     TCGA-69-7974     TCGA-69-8254 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-71-6725     TCGA-71-8520     TCGA-73-4659     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-73-7499     TCGA-75-5122     TCGA-83-5908     TCGA-86-6562 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-6851     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7953     TCGA-86-7954     TCGA-86-7955 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8054     TCGA-86-8055     TCGA-86-8056     TCGA-86-8073 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8074     TCGA-86-8075     TCGA-86-8076     TCGA-86-8278 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8279     TCGA-86-8280     TCGA-86-8281     TCGA-86-8358 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6829 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-91-6849     TCGA-93-7347     TCGA-93-7348     TCGA-93-A4JN 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-93-A4JO     TCGA-95-7567     TCGA-99-7458     TCGA-MN-A4N4 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MN-A4N5 
"NRAS WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NRAS MUTATED                            1                                 0
  NRAS WILD-TYPE                         16                               102
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NRAS MUTATED                                                    2
  NRAS WILD-TYPE                                                294
                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                                     16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            294
  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            256 
    TCGA-05-4384     TCGA-05-4396     TCGA-05-4405     TCGA-05-4410 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4427     TCGA-05-5420     TCGA-38-7271     TCGA-44-6147 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-6776     TCGA-44-7661     TCGA-44-7670     TCGA-44-8119 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-A47F     TCGA-55-1592     TCGA-55-1595     TCGA-55-7724 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7725     TCGA-55-7726     TCGA-55-7914     TCGA-55-8205 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8511     TCGA-55-8621     TCGA-55-A48X     TCGA-55-A491 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-A492     TCGA-64-1677     TCGA-73-4662     TCGA-73-7498 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7166     TCGA-78-7633     TCGA-78-8660     TCGA-80-5607 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-91-6836     TCGA-91-A4BC     TCGA-93-8067     TCGA-93-A4JQ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-95-7043     TCGA-95-7562     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-97-8172     TCGA-97-A4LX 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-97-A4M2     TCGA-97-A4M3     TCGA-97-A4M7     TCGA-J2-8194 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MP-A4T8 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-05-4390     TCGA-05-4415 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4417     TCGA-05-4424     TCGA-05-4433     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-A44F     TCGA-44-2656 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-2657     TCGA-44-3396     TCGA-44-3398     TCGA-44-3918 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-4112     TCGA-44-5644     TCGA-44-5645     TCGA-44-6144 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-6145     TCGA-44-6148     TCGA-44-6774     TCGA-44-6775 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-6777     TCGA-44-6778     TCGA-44-6779     TCGA-44-7659 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-7660     TCGA-44-7662     TCGA-44-7667     TCGA-44-7669 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-7672     TCGA-44-8117     TCGA-44-8120     TCGA-44-A479 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-A47A     TCGA-44-A47B     TCGA-44-A47G     TCGA-44-A4SS 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-A4SU     TCGA-49-4486     TCGA-49-4494     TCGA-49-4505 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-53-7624     TCGA-53-7626     TCGA-53-7813     TCGA-53-A4EZ 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-5899     TCGA-55-6642     TCGA-55-6712     TCGA-55-6971 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7227     TCGA-55-7283     TCGA-55-7570     TCGA-55-7574 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7576     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-55-7913     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-55-8299 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8301     TCGA-55-8302     TCGA-55-8506     TCGA-55-8507 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8512     TCGA-55-8514     TCGA-55-8615     TCGA-55-8620 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-A48Y     TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A493 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-A494     TCGA-62-8398     TCGA-64-1681     TCGA-64-5774 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-64-5775     TCGA-64-5778     TCGA-64-5779     TCGA-64-5781 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-69-7761     TCGA-69-7763     TCGA-69-7764     TCGA-69-7765 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-69-7974     TCGA-69-8253     TCGA-69-8255     TCGA-69-A59K 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-73-4659     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-75-6214     TCGA-75-7025 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-75-7027     TCGA-75-7031     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-78-7167 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7220     TCGA-78-7535     TCGA-78-7536     TCGA-78-7537 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7539     TCGA-78-7542     TCGA-78-8640     TCGA-78-8648 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-8655     TCGA-78-8662     TCGA-80-5608     TCGA-83-5908 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-6851     TCGA-86-7711     TCGA-86-7714     TCGA-86-7954 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8054     TCGA-86-8055     TCGA-86-8056     TCGA-86-8073 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8074     TCGA-86-8281     TCGA-86-8358     TCGA-86-8359 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8669     TCGA-86-8673     TCGA-86-8674     TCGA-86-A456 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-91-6829     TCGA-91-6830     TCGA-91-6840     TCGA-91-6849 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-91-8499     TCGA-93-7347     TCGA-93-7348     TCGA-93-A4JN 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-93-A4JO     TCGA-95-7567     TCGA-95-7944     TCGA-95-A4VP 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-97-7546     TCGA-97-7553     TCGA-97-7554     TCGA-97-7941 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-97-8171     TCGA-97-8174     TCGA-97-8176     TCGA-97-8179 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-97-A4M0     TCGA-97-A4M1     TCGA-97-A4M5     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-A4AD 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6     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-A4T9     TCGA-MP-A4TE 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4TF     TCGA-MP-A4TH     TCGA-MP-A4TI     TCGA-MP-A4TK 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A5C7     TCGA-NJ-A4YG     TCGA-NJ-A4YI     TCGA-O1-A52J 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
                vv
clus              R0  R1  R2  RX
  NRAS MUTATED     2   0   0   0
  NRAS WILD-TYPE 310  12   4  25
D42V13, multiclass
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             2            351 
    TCGA-05-4382     TCGA-05-4384     TCGA-05-4396     TCGA-05-4402 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4405     TCGA-05-4410     TCGA-05-4418     TCGA-05-4427 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4434     TCGA-05-5420     TCGA-38-4629     TCGA-38-4630 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-38-4631     TCGA-38-6178     TCGA-38-7271     TCGA-44-2661 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-49-4501     TCGA-49-6742     TCGA-49-6761     TCGA-50-6597 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-1592     TCGA-55-7284     TCGA-55-7724     TCGA-55-7725 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7726     TCGA-55-7914     TCGA-55-8090     TCGA-55-8091 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8203     TCGA-55-8204     TCGA-55-8205     TCGA-55-8207 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8511     TCGA-55-8619     TCGA-55-8621     TCGA-55-A48X 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-A491     TCGA-55-A492     TCGA-55-A4DF     TCGA-64-1677 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-67-6217     TCGA-73-4658     TCGA-73-4662     TCGA-73-7498 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7166     TCGA-78-7633     TCGA-78-8660     TCGA-80-5607 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-80-5611     TCGA-93-8067     TCGA-93-A4JQ     TCGA-95-7562 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-95-7947     TCGA-95-7948     TCGA-95-A4VK     TCGA-95-A4VN 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-97-A4M2     TCGA-97-A4M7     TCGA-L9-A443     TCGA-L9-A444 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MP-A4T8     TCGA-MP-A4TA     TCGA-MP-A4TC 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4TD     TCGA-05-4244     TCGA-05-4249     TCGA-05-4250 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4389     TCGA-05-4390     TCGA-05-4395     TCGA-05-4397 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4398     TCGA-05-4403     TCGA-05-4415     TCGA-05-4417 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4420     TCGA-05-4422     TCGA-05-4424     TCGA-05-4425 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-4426     TCGA-05-4430     TCGA-05-4432     TCGA-05-4433 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-5423     TCGA-05-5425     TCGA-05-5428     TCGA-05-5429 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-05-5715     TCGA-35-4122     TCGA-35-5375     TCGA-38-4625 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-38-4626     TCGA-38-4627     TCGA-38-4628     TCGA-38-A44F 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-2657     TCGA-44-2665     TCGA-44-3396     TCGA-44-3398 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-3918     TCGA-44-3919     TCGA-44-4112     TCGA-44-6144 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-6148     TCGA-44-6775     TCGA-44-A479     TCGA-44-A47A 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-44-A47B     TCGA-44-A47G     TCGA-44-A4SU     TCGA-49-4486 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-49-4487     TCGA-49-4488     TCGA-49-4494     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-49-6744     TCGA-49-6767     TCGA-50-5051 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-50-5055     TCGA-50-5066     TCGA-50-5931     TCGA-50-5942 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-50-5944     TCGA-50-6593     TCGA-50-6673     TCGA-50-8460 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-53-7624     TCGA-53-7626     TCGA-53-A4EZ     TCGA-55-5899 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-6642     TCGA-55-6712     TCGA-55-6970     TCGA-55-6971 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-6972     TCGA-55-6980     TCGA-55-6981     TCGA-55-6983 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-6985     TCGA-55-7227     TCGA-55-7281     TCGA-55-7570 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7574     TCGA-55-7576     TCGA-55-7727     TCGA-55-7728 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7815     TCGA-55-7903     TCGA-55-7907     TCGA-55-7910 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-7911     TCGA-55-7913     TCGA-55-7994     TCGA-55-7995 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8085     TCGA-55-8087     TCGA-55-8089     TCGA-55-8092 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8094     TCGA-55-8097     TCGA-55-8206     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-55-8512     TCGA-55-8513     TCGA-55-8514     TCGA-55-8614 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-8615     TCGA-55-8616     TCGA-55-8620     TCGA-55-A48Y 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A493     TCGA-55-A494 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-55-A4DG     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-64-1676     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-71-6725 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     TCGA-73-4666     TCGA-73-4668 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-73-4670     TCGA-73-4675     TCGA-73-4676     TCGA-73-4677 
"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-78-7167 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7220     TCGA-78-7535     TCGA-78-7536     TCGA-78-7537 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-7539     TCGA-78-7540     TCGA-78-7542     TCGA-78-8640 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-78-8648     TCGA-78-8655     TCGA-78-8662     TCGA-80-5608 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-83-5908     TCGA-86-6562     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-86-8358 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8585     TCGA-86-8668     TCGA-86-8669 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-8671     TCGA-86-8672     TCGA-86-8673     TCGA-86-8674 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6828 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-91-6829     TCGA-91-6835     TCGA-91-6840     TCGA-91-A4BD 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-93-7347     TCGA-93-7348     TCGA-93-A4JN     TCGA-93-A4JO 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-93-A4JP     TCGA-95-7944     TCGA-95-8039     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-99-7458     TCGA-99-8025     TCGA-99-8028     TCGA-99-8032 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-99-8033     TCGA-J2-A4AD     TCGA-J2-A4AE     TCGA-J2-A4AG 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-L4-A4E5     TCGA-L4-A4E6     TCGA-MN-A4N4     TCGA-MN-A4N5 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4SY     TCGA-MP-A4T2 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4T4     TCGA-MP-A4T6     TCGA-MP-A4T7     TCGA-MP-A4T9 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4TE     TCGA-MP-A4TF     TCGA-MP-A4TH     TCGA-MP-A4TI 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-MP-A4TK     TCGA-MP-A5C7     TCGA-NJ-A4YQ 
"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                        29   376
D42V14, multiclass
                                  clus
vv                                 NRAS MUTATED NRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             29
  WHITE                                       2            376
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V15, binary
                cls
clus               0   1
  NRAS MUTATED     0   3
  NRAS WILD-TYPE   6 348
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      0    3
  NRAS WILD-TYPE    6  348
                        clus
vv                       NRAS MUTATED NRAS WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            3            348
[1] 2 2
[1] FALSE

Clustering(43) Variable = G3BP1 MUTATION ANALYSIS
D43V1, survival
                 sevent
clus2               0   1
  G3BP1 MUTATED     4   3
  G3BP1 WILD-TYPE 294 168
  G3BP1 MUTATED G3BP1 WILD-TYPE 
              7             462 
  G3BP1 MUTATED G3BP1 WILD-TYPE 
              3             168 
$`G3BP1 MUTATED`
TCGA-44-2661 TCGA-05-4432 TCGA-49-4486 TCGA-50-5044 TCGA-50-6594 TCGA-53-A4EZ 
       38.10        25.02        76.21        20.52        12.16        35.21 
TCGA-67-3771 
       20.05 

$`G3BP1 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       14.73        26.30        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       29.98        12.00        30.02        21.99        26.01        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         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-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       22.26        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       49.28         8.22         9.27        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
        3.91        25.55        11.05         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99        36.79        27.25        34.29        30.54        13.94 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       30.58        14.30        80.52         5.62        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       15.25        46.03        53.65         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       31.30        28.67        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        3.91        23.15        25.41        15.39        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       34.19        17.65        18.44        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       15.19        23.08         5.06        17.79        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       29.19        22.16        15.42        17.56        15.72        14.47 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36        13.74        20.28        17.72        19.96        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
       17.10        17.62        14.66         1.58        12.33        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 
       21.40         3.25         0.92        15.81        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-64-1679 TCGA-64-1681 
       39.25        40.96        29.92        56.81        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-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       18.84        14.04        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41        13.41        13.51        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       19.43         8.42         6.90        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 
        4.31        30.31         9.24         1.25        50.33        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       77.85        43.82        85.15        49.84        36.66       108.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
      100.57       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-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      238.29        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       26.01        39.35        10.55       232.18        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
      110.50        93.11        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 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 
       11.61        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-91-6840 TCGA-91-6847 
       41.36         1.97        10.19         2.60        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
        7.36         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       22.45        17.46        23.61         1.08        19.00        41.82 
TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 
       18.67        12.39        27.29         2.76        19.89        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        61.48        25.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       15.91        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       14.30        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 
       18.08        35.47        32.48        19.00        14.30        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.85         5.49        41.59        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        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        47.08         0.49         0.43        19.82        59.11 

  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          21.455 
[1] "12.2 - 76.2 (25.0)" "0.0 - 238.3 (21.5)"
[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      118      132        45        65         68
                 vv
clus              STAGE IIIB STAGE IV
  G3BP1 MUTATED            1        0
  G3BP1 WILD-TYPE         10       24
D43V3, multiclass
            clus
vv           G3BP1 MUTATED G3BP1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             118
  STAGE IB               0             132
  STAGE IIA              1              45
  STAGE IIB              1              65
  STAGE IIIA             2              68
  STAGE IIIB             1              10
  STAGE IV               0              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
  G3BP1 MUTATED     3   2   2   1
  G3BP1 WILD-TYPE 153 259  41  17
D43V4, multiclass
    clus
vv   G3BP1 MUTATED G3BP1 WILD-TYPE
  T1             3             153
  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 305  86    70
D43V5, multiclass
       clus
vv      G3BP1 MUTATED G3BP1 WILD-TYPE
  N0                3             305
  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 255 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP1 MUTATED      5    3
  G3BP1 WILD-TYPE  255  218
        clus
vv       G3BP1 MUTATED G3BP1 WILD-TYPE
  FEMALE             5             255
  MALE               3             218
[1] 2 2
[1] FALSE
D43V8, binary
                 cls
clus                0   1
  G3BP1 MUTATED     5   2
  G3BP1 WILD-TYPE 379  53
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP1 MUTATED      5    2
  G3BP1 WILD-TYPE  379   53
     clus
vv    G3BP1 MUTATED G3BP1 WILD-TYPE
  NO              5             379
  YES             2              53
[1] 2 2
[1] FALSE
D43V9, continuous
[1] "Remove cluster labels:" "G3BP1 MUTATED"         
clus
  G3BP1 MUTATED G3BP1 WILD-TYPE 
              2             120 
     TCGA-44-6147      TCGA-44-A47F      TCGA-49-6742      TCGA-55-7573 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7914      TCGA-55-8205      TCGA-55-8511 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8621      TCGA-55-A491      TCGA-55-A492 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-64-1677      TCGA-73-4662      TCGA-73-7498      TCGA-93-8067 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-35-4122      TCGA-35-4123      TCGA-35-5375 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-3396      TCGA-44-3918      TCGA-44-4112      TCGA-44-6144 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-7660      TCGA-49-4494      TCGA-49-4505 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-49-4506      TCGA-49-4510      TCGA-49-6743      TCGA-49-6744 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-53-7624      TCGA-55-5899      TCGA-55-7283      TCGA-55-7574 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-7910      TCGA-55-7913      TCGA-55-7995      TCGA-55-8089 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-8096      TCGA-55-8208      TCGA-55-8507      TCGA-55-8508 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8513      TCGA-55-8620      TCGA-55-A48Z 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-A490      TCGA-55-A494      TCGA-62-8394      TCGA-62-8395 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-62-8397      TCGA-62-8398      TCGA-62-8399      TCGA-62-8402 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R      TCGA-62-A46S 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y      TCGA-62-A470 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-62-A471      TCGA-62-A472      TCGA-64-1681      TCGA-64-5775 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-64-5778      TCGA-69-7974      TCGA-69-8254      TCGA-71-6725 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-71-8520      TCGA-73-4659      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-73-7499 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-75-5122      TCGA-83-5908      TCGA-86-6562      TCGA-86-6851 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-7701      TCGA-86-7711      TCGA-86-7713      TCGA-86-7714 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-7953      TCGA-86-7954      TCGA-86-7955      TCGA-86-8054 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8073      TCGA-86-8074 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-8075      TCGA-86-8076      TCGA-86-8278      TCGA-86-8279 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-8280      TCGA-86-8281      TCGA-86-8358      TCGA-86-8359 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-A456 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6829      TCGA-91-6849 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-93-7347      TCGA-93-7348      TCGA-93-A4JN      TCGA-93-A4JO 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-95-7567      TCGA-99-7458      TCGA-MN-A4N4      TCGA-MN-A4N5 
"G3BP1 WILD-TYPE" "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                         16                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  G3BP1 MUTATED                                                    5
  G3BP1 WILD-TYPE                                                291
                 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                                      16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  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                                   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             256 
     TCGA-05-4384      TCGA-05-4396      TCGA-05-4405      TCGA-05-4410 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-05-4427      TCGA-05-5420      TCGA-38-7271      TCGA-44-6147 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-6776      TCGA-44-7661      TCGA-44-7670      TCGA-44-8119 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-A47F      TCGA-55-1592      TCGA-55-1595      TCGA-55-7724 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7726      TCGA-55-7914      TCGA-55-8205 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-8511      TCGA-55-8621      TCGA-55-A48X      TCGA-55-A491 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-A492      TCGA-64-1677      TCGA-73-4662      TCGA-73-7498 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7166      TCGA-78-7633      TCGA-78-8660      TCGA-80-5607 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-91-6836      TCGA-91-A4BC      TCGA-93-8067      TCGA-93-A4JQ 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-95-7043      TCGA-95-7562      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-97-8172      TCGA-97-A4LX 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-97-A4M2      TCGA-97-A4M3      TCGA-97-A4M7      TCGA-J2-8194 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-L9-A443      TCGA-L9-A444      TCGA-MN-A4N1      TCGA-MP-A4T8 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-MP-A4TA      TCGA-MP-A4TC      TCGA-05-4390      TCGA-05-4415 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-05-4417      TCGA-05-4424      TCGA-05-4433      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-A44F 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-2656      TCGA-44-2657      TCGA-44-3396      TCGA-44-3398 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-3918      TCGA-44-4112      TCGA-44-5644      TCGA-44-5645 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-6144      TCGA-44-6145      TCGA-44-6148      TCGA-44-6774 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-6777      TCGA-44-6778      TCGA-44-6779 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-7659      TCGA-44-7660      TCGA-44-7662      TCGA-44-7667 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-7669      TCGA-44-7672      TCGA-44-8117      TCGA-44-8120 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-A479      TCGA-44-A47A      TCGA-44-A47B      TCGA-44-A47G 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-44-A4SS      TCGA-44-A4SU      TCGA-49-4494      TCGA-49-4505 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-53-7624      TCGA-53-7626      TCGA-53-7813      TCGA-55-5899 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-6642      TCGA-55-6712      TCGA-55-6971      TCGA-55-7227 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7570      TCGA-55-7574      TCGA-55-7576 
"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-55-7913      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-55-8299      TCGA-55-8301 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-8302      TCGA-55-8506      TCGA-55-8507      TCGA-55-8512 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-8514      TCGA-55-8615      TCGA-55-8620      TCGA-55-A48Y 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A493      TCGA-55-A494 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-62-8398      TCGA-64-1681      TCGA-64-5774      TCGA-64-5775 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-64-5778      TCGA-64-5779      TCGA-64-5781      TCGA-69-7761 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-69-7763      TCGA-69-7764      TCGA-69-7765      TCGA-69-7974 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-69-7979      TCGA-69-8253      TCGA-69-8255      TCGA-69-A59K 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-73-4659      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-75-6214      TCGA-75-7025 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-75-7027      TCGA-75-7031      TCGA-78-7145      TCGA-78-7146 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7147      TCGA-78-7148      TCGA-78-7149      TCGA-78-7150 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7152      TCGA-78-7153      TCGA-78-7154      TCGA-78-7155 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7156      TCGA-78-7158      TCGA-78-7159      TCGA-78-7160 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7161      TCGA-78-7162      TCGA-78-7163      TCGA-78-7167 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7220      TCGA-78-7535      TCGA-78-7536      TCGA-78-7537 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-7539      TCGA-78-7542      TCGA-78-8640      TCGA-78-8648 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-78-8655      TCGA-78-8662      TCGA-80-5608      TCGA-83-5908 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-6851      TCGA-86-7711      TCGA-86-7714      TCGA-86-7954 
"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-86-8281      TCGA-86-8358      TCGA-86-8359 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-86-8669      TCGA-86-8673      TCGA-86-8674      TCGA-86-A456 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-91-6829      TCGA-91-6830      TCGA-91-6840      TCGA-91-6849 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-91-8499      TCGA-93-7347      TCGA-93-7348      TCGA-93-A4JN 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-93-A4JO      TCGA-95-7567      TCGA-95-7944      TCGA-95-A4VP 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-97-7546      TCGA-97-7553      TCGA-97-7554      TCGA-97-7941 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-97-8171      TCGA-97-8174      TCGA-97-8176      TCGA-97-8179 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-97-A4M0      TCGA-97-A4M1      TCGA-97-A4M5      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-A4AD 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-J2-A4AG      TCGA-L4-A4E5      TCGA-L4-A4E6      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-A4T9      TCGA-MP-A4TE 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-MP-A4TF      TCGA-MP-A4TH      TCGA-MP-A4TI      TCGA-MP-A4TK 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
     TCGA-MP-A5C7      TCGA-NJ-A4YG      TCGA-NJ-A4YI      TCGA-O1-A52J 
"G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" "G3BP1 WILD-TYPE" 
                 vv
clus               R0  R1  R2  RX
  G3BP1 MUTATED     4   0   1   1
  G3BP1 WILD-TYPE 308  12   3  24
D43V13, multiclass
    clus
vv   G3BP1 MUTATED G3BP1 WILD-TYPE
  R0             4             308
  R1             0              12
  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                        28   374
D43V14, multiclass
                                  clus
vv                                 G3BP1 MUTATED G3BP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              28
  WHITE                                        4             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"
D43V15, binary
                 cls
clus                0   1
  G3BP1 MUTATED     1   5
  G3BP1 WILD-TYPE   5 346
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP1 MUTATED      1    5
  G3BP1 WILD-TYPE    5  346
                        clus
vv                       G3BP1 MUTATED G3BP1 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             5             346
[1] 2 2
[1] FALSE

Clustering(44) Variable = TRERF1 MUTATION ANALYSIS
D44V1, survival
                  sevent
clus2                0   1
  TRERF1 MUTATED     8  10
  TRERF1 WILD-TYPE 290 161
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              18              451 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
              10              161 
$`TRERF1 MUTATED`
TCGA-05-5420 TCGA-44-7670 TCGA-55-8204 TCGA-55-8511 TCGA-64-1677 TCGA-93-8067 
       15.02        29.00        16.93        18.15        20.65         6.12 
TCGA-J2-8194 TCGA-05-4250 TCGA-49-4488 TCGA-55-7907 TCGA-62-A46O TCGA-69-7978 
       23.80         3.98        28.57        11.28        47.80         4.41 
TCGA-78-7145 TCGA-78-7155 TCGA-78-7220 TCGA-78-8662 TCGA-95-8494 TCGA-O1-A52J 
       27.16        38.50        26.53       110.50         2.76        59.11 

$`TRERF1 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       26.01        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       29.23         9.37        11.08        46.72        16.04        17.16 
TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 
       11.64        40.60        21.47        41.69        23.05        48.62 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        5.79         7.79         7.99        16.01        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8205 
       21.44         6.15        19.66        19.73        17.98        19.69 
TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 
       32.12        13.68        16.93        22.65        20.58        19.59 
TCGA-55-A4DF TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       20.19        13.87        52.60        82.68        39.09         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
       50.24        10.55        85.32        13.71        16.18         1.45 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       17.29        16.54         2.86        15.68        15.65        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       18.18        17.92        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       24.30         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        2.43        10.09        50.07        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         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-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       76.21        28.11        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        48.46        60.72        57.53        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99        36.79        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       30.54        13.94        35.21        30.58        14.30        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        5.62        42.51        40.73        15.25        46.03        53.65 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26        31.30        28.67        20.02 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       27.09        32.71        22.03         3.91        23.15        25.41 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       15.39        18.64        34.19        17.65        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       29.23        29.72        15.19        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.72        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       19.96        26.01        17.10        17.62        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       12.33        20.71        21.40         3.25         0.92        15.81 
TCGA-55-A4DG TCGA-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-64-1679 
       13.61        39.25        40.96        29.92        56.81        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05        13.41        13.51        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 
        4.24        19.43         8.42         6.90        23.38        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-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 
       66.64        77.85        43.82        85.15        49.84        36.66 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
      108.66       100.57       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-78-7167 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-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 TCGA-83-5908 
       10.55       232.18        39.75        77.59        93.11        27.09 
TCGA-86-6562 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        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
        1.08        19.00        41.82        18.67        12.39        27.29 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       15.39        16.41        14.30        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       19.76        20.84        18.67        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        1.45        21.57        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       14.30        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE 
       37.35        86.04        58.85         5.49        41.59        29.46 
TCGA-MP-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 
       74.33         0.13         1.64        47.08         0.49         0.43 
TCGA-NJ-A55R 
       19.82 

  TRERF1 MUTATED TRERF1 WILD-TYPE 
            2.76             0.00 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
          110.50           238.29 
  TRERF1 MUTATED TRERF1 WILD-TYPE 
          22.225           21.470 
[1] "2.8 - 110.5 (22.2)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.6"
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      119      126        43        64         66
                  vv
clus               STAGE IIIB STAGE IV
  TRERF1 MUTATED            0        1
  TRERF1 WILD-TYPE         11       23
D44V3, multiclass
            clus
vv           TRERF1 MUTATED TRERF1 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              119
  STAGE IB                6              126
  STAGE IIA               3               43
  STAGE IIB               2               64
  STAGE IIIA              4               66
  STAGE IIIB              0               11
  STAGE IV                1               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
  TRERF1 MUTATED     3  12   2   1
  TRERF1 WILD-TYPE 153 249  41  17
D44V4, multiclass
    clus
vv   TRERF1 MUTATED TRERF1 WILD-TYPE
  T1              3              153
  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 299  83    69
D44V5, multiclass
       clus
vv      TRERF1 MUTATED TRERF1 WILD-TYPE
  N0                 9              299
  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 248 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED     12    6
  TRERF1 WILD-TYPE  248  215
        clus
vv       TRERF1 MUTATED TRERF1 WILD-TYPE
  FEMALE             12              248
  MALE                6              215
[1] 2 2
[1] FALSE
D44V8, binary
                  cls
clus                 0   1
  TRERF1 MUTATED    13   2
  TRERF1 WILD-TYPE 371  53
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED     13    2
  TRERF1 WILD-TYPE  371   53
     clus
vv    TRERF1 MUTATED TRERF1 WILD-TYPE
  NO              13              371
  YES              2               53
[1] 2 2
[1] FALSE
D44V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TRERF1 MUTATED                            0                                 3
  TRERF1 WILD-TYPE                         17                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TRERF1 MUTATED                                                   15
  TRERF1 WILD-TYPE                                                281
                  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                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              281
  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 302  11   3  24
D44V13, multiclass
    clus
vv   TRERF1 MUTATED TRERF1 WILD-TYPE
  R0             10              302
  R1              1               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
  TRERF1 MUTATED                                  0     1
  TRERF1 WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRERF1 MUTATED                           0    14
  TRERF1 WILD-TYPE                        30   364
D44V14, multiclass
                                  clus
vv                                 TRERF1 MUTATED TRERF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     0               30
  WHITE                                        14              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"
D44V15, binary
                  cls
clus                 0   1
  TRERF1 MUTATED     1  11
  TRERF1 WILD-TYPE   5 340
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRERF1 MUTATED      1   11
  TRERF1 WILD-TYPE    5  340
                        clus
vv                       TRERF1 MUTATED TRERF1 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             11              340
[1] 2 2
[1] FALSE

Clustering(45) Variable = CACNA1F MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  CACNA1F MUTATED    18   9
  CACNA1F WILD-TYPE 280 162
  CACNA1F MUTATED CACNA1F WILD-TYPE 
               27               442 
  CACNA1F MUTATED CACNA1F WILD-TYPE 
                9               162 
$`CACNA1F MUTATED`
TCGA-05-4402 TCGA-38-4631 TCGA-55-8203 TCGA-55-8511 TCGA-55-A48X TCGA-78-7166 
        8.02        11.64        17.98        18.15        22.65         8.48 
TCGA-95-A4VN TCGA-L9-A444 TCGA-44-A4SS TCGA-49-4514 TCGA-49-6743 TCGA-50-5045 
       18.18        10.09        13.64        55.89        53.29        71.47 
TCGA-53-A4EZ TCGA-55-7281 TCGA-55-8301 TCGA-62-A46R TCGA-64-5778 TCGA-64-5815 
       35.21        28.67        17.56        56.71        42.90        28.47 
TCGA-69-7979 TCGA-69-A59K TCGA-75-6214 TCGA-78-7147 TCGA-78-7220 TCGA-91-8497 
       13.41        19.43        36.66        19.27        26.53        14.27 
TCGA-97-7546 TCGA-97-7941 TCGA-MN-A4N4 
       42.25        15.91        38.63 

$`CACNA1F WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 
       15.02        15.02        28.41        35.28        14.73        26.30 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       38.10        23.93        27.78        86.01        18.31        29.00 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       29.23         9.37        11.08        46.72        16.04        17.16 
TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 
       11.64        40.60        21.47        41.69        23.05        48.62 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        5.79         7.79         7.99        16.01        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8204 TCGA-55-8205 
       21.44         6.15        19.66        19.73        16.93        19.69 
TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF 
       32.12        13.68        16.93        20.58        19.59        20.19 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7633 
       20.65        13.87        52.60        82.68        39.09        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       17.29        16.54         2.86        15.68        15.65        21.40 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
       23.80         6.35        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         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-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 
       15.98        15.32         9.44        11.54        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 
        8.81        29.46        29.75        55.33        22.26        20.52 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
      101.72        15.72        60.16        47.41        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        9.27        14.27        78.67         8.45        15.12        48.46 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       60.72        57.53        53.16        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05        12.16         6.21         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-5899 
       36.79        27.25        34.29        30.54        13.94        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       14.30        80.52         5.62        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       46.03        53.65         3.88        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       92.81        24.99        40.54       107.21        70.26        31.30 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       20.02        27.09        32.71        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       25.41        15.39        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.44        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       15.42        15.72        14.47         0.36        13.74        20.28 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
        1.58        12.33        20.71        21.40         3.25         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U 
       88.64        49.25        47.80        19.53        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       72.30        13.61        39.25        40.96        29.92        56.81 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 
       81.80        38.37        87.98         2.04        28.41        51.25 
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-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         4.41        13.51        14.01        13.45         4.24 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        8.42         6.90        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       30.31         9.24         1.25        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       43.82        85.15        49.84       108.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
       27.16         5.69        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 
       22.92         9.57       104.19       238.29        88.14        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59       110.50        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8499 
       12.23        27.68         7.36         1.15        16.60         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45        17.46        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       41.82        18.67        12.39        27.29         2.76        19.89 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        61.48        25.48        18.54         0.59 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       21.60        20.58        21.44        19.76        20.84        18.67 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
       24.56        34.85        36.76         1.45        21.57        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N5 TCGA-MP-A4SV 
       35.47        32.48        19.00        14.30         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       41.59        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.49         0.43        19.82        59.11 

  CACNA1F MUTATED CACNA1F WILD-TYPE 
             8.02              0.00 
  CACNA1F MUTATED CACNA1F WILD-TYPE 
            71.47            238.29 
  CACNA1F MUTATED CACNA1F WILD-TYPE 
            19.43             21.47 
[1] "8.0 - 71.5 (19.4)"  "0.0 - 238.3 (21.5)"
[1] "hr=" "1.1"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CACNA1F MUTATED         0        9        6         3         4          3
  CACNA1F WILD-TYPE       4      112      126        43        62         67
                   vv
clus                STAGE IIIB STAGE IV
  CACNA1F MUTATED            0        1
  CACNA1F WILD-TYPE         11       23
D45V3, multiclass
            clus
vv           CACNA1F MUTATED CACNA1F WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 9               112
  STAGE IB                 6               126
  STAGE IIA                3                43
  STAGE IIB                4                62
  STAGE IIIA               3                67
  STAGE IIIB               0                11
  STAGE IV                 1                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
  CACNA1F MUTATED    11  15   1   0
  CACNA1F WILD-TYPE 145 246  42  18
D45V4, multiclass
    clus
vv   CACNA1F MUTATED CACNA1F WILD-TYPE
  T1              11               145
  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 292  82    69
D45V5, multiclass
       clus
vv      CACNA1F MUTATED CACNA1F WILD-TYPE
  N0                 16               292
  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 240 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1F MUTATED     20    7
  CACNA1F WILD-TYPE  240  214
        clus
vv       CACNA1F MUTATED CACNA1F WILD-TYPE
  FEMALE              20               240
  MALE                 7               214
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  CACNA1F MUTATED    22   5
  CACNA1F WILD-TYPE 362  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1F MUTATED     22    5
  CACNA1F WILD-TYPE  362   50
     clus
vv    CACNA1F MUTATED CACNA1F WILD-TYPE
  NO               22               362
  YES               5                50
[1] 2 2
[1] FALSE
D45V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  CACNA1F MUTATED                            4
  CACNA1F WILD-TYPE                         13
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  CACNA1F MUTATED                                   5
  CACNA1F WILD-TYPE                                97
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CACNA1F MUTATED                                                   14
  CACNA1F WILD-TYPE                                                282
                   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                                        13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 97
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               282
  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 293  12   3  24
D45V13, multiclass
    clus
vv   CACNA1F MUTATED CACNA1F WILD-TYPE
  R0              19               293
  R1               0                12
  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                        28   355
D45V14, multiclass
                                  clus
vv                                 CACNA1F MUTATED CACNA1F WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      2                28
  WHITE                                         23               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"
D45V15, binary
                   cls
clus                  0   1
  CACNA1F MUTATED     1  18
  CACNA1F WILD-TYPE   5 333
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1F MUTATED      1   18
  CACNA1F WILD-TYPE    5  333
                        clus
vv                       CACNA1F MUTATED CACNA1F WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO              18               333
[1] 2 2
[1] FALSE

Clustering(46) Variable = NFE2L2 MUTATION ANALYSIS
D46V1, survival
                  sevent
clus2                0   1
  NFE2L2 MUTATED     6   7
  NFE2L2 WILD-TYPE 292 164
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              13              456 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               7              164 
$`NFE2L2 MUTATED`
TCGA-73-4658 TCGA-78-8660 TCGA-93-8067 TCGA-05-4422 TCGA-50-5930 TCGA-55-6975 
       52.60        10.55         6.12        12.00         9.27         3.88 
TCGA-55-6982 TCGA-55-A48Y TCGA-62-8395 TCGA-62-A471 TCGA-97-7941 TCGA-97-8174 
       32.71        20.71        39.98        40.96        15.91         5.39 
TCGA-J2-A4AD 
       18.08 

$`NFE2L2 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-80-5611 
       13.87        82.68        39.09         8.48        50.24        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       13.71        16.18         1.45        17.29        16.54         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       15.68        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       10.09        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 
       47.05        19.00         2.99        14.96        29.98        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 
       21.99        26.01        25.02        25.02        24.00         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 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-38-4632 
        8.68        97.74       120.79        37.71        49.05        44.61 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
        4.37        46.98        44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       23.77        19.56        23.15        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
       61.28        16.44        22.72        19.46         7.17        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       18.87        23.64        12.66         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
        9.44        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 
       29.46        29.75        55.89        53.29        55.33        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
       49.28         8.22        14.27        78.67         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       48.46        60.72        57.53        53.16        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05        12.16         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99        36.79        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       35.21        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6981 
       40.73        15.25        46.03        53.65        69.34        45.34 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       92.81        24.99        40.54       107.21        70.26        31.30 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
       28.67        20.02        27.09        32.71        22.03         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
       23.15        25.41        15.39        18.64        11.28        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       23.08         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       13.74        20.28        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 
       17.62        14.66         1.58        12.33        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 
        0.92        15.81        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-A472 TCGA-64-1676 
       67.96        72.30        13.61        39.25        29.92        56.81 
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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        19.43         8.42         6.90 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       23.38        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
        1.25        50.33        66.64        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       49.84        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
       22.92         9.57       104.19       238.29        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
        1.08        19.00        41.82        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 
       25.48        18.54         0.59        18.67        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 
       21.57        35.47        32.48        19.00        14.30        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.85         5.49        41.59        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        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        47.08         0.49         0.43        19.82        59.11 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            3.88             0.00 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           52.60           238.29 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
          15.910           21.585 
[1] "3.9 - 52.6 (15.9)"  "0.0 - 238.3 (21.6)"
[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      119      129        44        61         69
                  vv
clus               STAGE IIIB STAGE IV
  NFE2L2 MUTATED            0        0
  NFE2L2 WILD-TYPE         11       24
D46V3, multiclass
            clus
vv           NFE2L2 MUTATED NFE2L2 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              119
  STAGE IB                3              129
  STAGE IIA               2               44
  STAGE IIB               5               61
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               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
  NFE2L2 MUTATED     2  10   1   0
  NFE2L2 WILD-TYPE 154 251  42  18
D46V4, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  T1              2              154
  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 300  85    71
D46V5, multiclass
       clus
vv      NFE2L2 MUTATED NFE2L2 WILD-TYPE
  N0                 8              300
  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 255 213
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      5    8
  NFE2L2 WILD-TYPE  255  213
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  FEMALE              5              255
  MALE                8              213
[1] 2 2
[1] FALSE
D46V8, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED    10   2
  NFE2L2 WILD-TYPE 374  53
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED     10    2
  NFE2L2 WILD-TYPE  374   53
     clus
vv    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  NO              10              374
  YES              2               53
[1] 2 2
[1] FALSE
D46V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  NFE2L2 MUTATED                            1                                 4
  NFE2L2 WILD-TYPE                         16                                98
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NFE2L2 MUTATED                                                    7
  NFE2L2 WILD-TYPE                                                289
                  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                                       16
  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                                    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 305  12   4  23
D46V13, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  R0              7              305
  R1              0               12
  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                        30   368
D46V14, multiclass
                                  clus
vv                                 NFE2L2 MUTATED NFE2L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     0               30
  WHITE                                        10              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"
D46V15, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     0  10
  NFE2L2 WILD-TYPE   6 341
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      0   10
  NFE2L2 WILD-TYPE    6  341
                        clus
vv                       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             10              341
[1] 2 2
[1] FALSE

Clustering(47) Variable = RPL5 MUTATION ANALYSIS
D47V1, survival
                sevent
clus2              0   1
  RPL5 MUTATED     5   2
  RPL5 WILD-TYPE 293 169
  RPL5 MUTATED RPL5 WILD-TYPE 
             7            462 
  RPL5 MUTATED RPL5 WILD-TYPE 
             2            169 
$`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-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       29.98        12.00        30.02        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       25.02        24.00         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       37.71        49.05        44.61         4.37        46.98        44.42 
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-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       19.46         7.17        36.07        18.87        23.64        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
        8.55        15.98        15.32         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       53.29        55.33        22.26        20.52        71.47       101.72 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        47.41        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       14.27        78.67         8.45        15.12        48.46        60.72 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       57.53        53.16        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       12.16         6.21         0.72        10.13        36.99        36.79 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 
       27.25        34.29        30.54        13.94        35.21        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       14.30        80.52         5.62        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       46.03        53.65         3.88        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       92.81        24.99        40.54       107.21        70.26        31.30 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
       28.67        20.02        27.09        32.71        22.03         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
       23.15        25.41        15.39        18.64        11.28        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65        18.44        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42        17.56        15.72        14.47         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       14.66         1.58        12.33        20.71        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 
        0.92        15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       56.81        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-69-7760 TCGA-69-7761 TCGA-69-7763 
       14.73         5.72         4.64         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        13.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       13.51        14.01        13.45         4.24        19.43         8.42 
TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        6.90        23.38        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
        9.24         1.25        50.33        66.64        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       85.15        49.84        36.66       108.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 
       64.90        22.92         9.57       104.19       238.29        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 TCGA-83-5908 
       10.55       232.18        39.75        77.59        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 TCGA-91-8497 
        2.60        12.23        27.68         7.36        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.18        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
       19.00        41.82        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       15.39        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.57        18.08        35.47        32.48        19.00        14.30 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J 
        0.13         1.64        47.08         0.49         0.43        59.11 

  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          21.52 
[1] "1.1 - 110.5 (19.8)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.4"
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      120      130        45        63         69
                vv
clus             STAGE IIIB STAGE IV
  RPL5 MUTATED            0        0
  RPL5 WILD-TYPE         11       24
D47V3, multiclass
            clus
vv           RPL5 MUTATED RPL5 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            120
  STAGE IB              2            130
  STAGE IIA             1             45
  STAGE IIB             3             63
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              0             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
  RPL5 MUTATED     1   4   3   0
  RPL5 WILD-TYPE 155 257  40  18
D47V4, multiclass
    clus
vv   RPL5 MUTATED RPL5 WILD-TYPE
  T1            1            155
  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 302  88    71
D47V5, multiclass
       clus
vv      RPL5 MUTATED RPL5 WILD-TYPE
  N0               6            302
  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 256 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL5 MUTATED      4    4
  RPL5 WILD-TYPE  256  217
        clus
vv       RPL5 MUTATED RPL5 WILD-TYPE
  FEMALE            4            256
  MALE              4            217
[1] 2 2
[1] FALSE
D47V8, binary
                cls
clus               0   1
  RPL5 MUTATED     7   0
  RPL5 WILD-TYPE 377  55
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL5 MUTATED      7    0
  RPL5 WILD-TYPE  377   55
     clus
vv    RPL5 MUTATED RPL5 WILD-TYPE
  NO             7            377
  YES            0             55
[1] 2 2
[1] FALSE
D47V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RPL5 MUTATED                            0                                 2
  RPL5 WILD-TYPE                         17                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RPL5 MUTATED                                                    5
  RPL5 WILD-TYPE                                                291
                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                                     17
  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                                    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            256 
    TCGA-05-4384     TCGA-05-4396     TCGA-05-4405     TCGA-05-4410 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-05-4427     TCGA-05-5420     TCGA-38-7271     TCGA-44-6147 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-6776     TCGA-44-7661     TCGA-44-7670     TCGA-44-8119 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-A47F     TCGA-55-1592     TCGA-55-1595     TCGA-55-7724 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-7725     TCGA-55-7726     TCGA-55-7914     TCGA-55-8205 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-8511     TCGA-55-8621     TCGA-55-A48X     TCGA-55-A491 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-A492     TCGA-64-1677     TCGA-73-4662     TCGA-73-7498 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-7166     TCGA-78-7633     TCGA-78-8660     TCGA-80-5607 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-91-6836     TCGA-91-A4BC     TCGA-93-8067     TCGA-93-A4JQ 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-95-7043     TCGA-95-7562     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-97-8172     TCGA-97-A4LX 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-97-A4M2     TCGA-97-A4M3     TCGA-97-A4M7     TCGA-J2-8194 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-L9-A443     TCGA-L9-A444     TCGA-MN-A4N1     TCGA-MP-A4T8 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-MP-A4TA     TCGA-MP-A4TC     TCGA-05-4390     TCGA-05-4415 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-05-4417     TCGA-05-4424     TCGA-05-4433     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-A44F 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-2656     TCGA-44-2657     TCGA-44-3396     TCGA-44-3398 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-3918     TCGA-44-4112     TCGA-44-5644     TCGA-44-5645 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-6144     TCGA-44-6145     TCGA-44-6148     TCGA-44-6774 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-6775     TCGA-44-6777     TCGA-44-6778     TCGA-44-6779 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-7659     TCGA-44-7660     TCGA-44-7662     TCGA-44-7667 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-7669     TCGA-44-7672     TCGA-44-8117     TCGA-44-8120 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-A479     TCGA-44-A47A     TCGA-44-A47B     TCGA-44-A47G 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-44-A4SS     TCGA-44-A4SU     TCGA-49-4486     TCGA-49-4494 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-49-4505     TCGA-53-7624     TCGA-53-7626     TCGA-53-7813 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-53-A4EZ     TCGA-55-5899     TCGA-55-6642     TCGA-55-6712 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-6971     TCGA-55-7227     TCGA-55-7283     TCGA-55-7570 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-7574     TCGA-55-7576     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-55-7913     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-55-8299     TCGA-55-8301     TCGA-55-8302     TCGA-55-8506 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-8507     TCGA-55-8512     TCGA-55-8514     TCGA-55-8615 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-8620     TCGA-55-A48Y     TCGA-55-A48Z     TCGA-55-A490 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-55-A493     TCGA-55-A494     TCGA-62-8398     TCGA-64-1681 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-64-5774     TCGA-64-5775     TCGA-64-5778     TCGA-64-5779 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-64-5781     TCGA-69-7761     TCGA-69-7763     TCGA-69-7764 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-69-7765     TCGA-69-7974     TCGA-69-7979     TCGA-69-8253 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-69-8255     TCGA-69-A59K     TCGA-73-4659     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-75-6214     TCGA-75-7025     TCGA-75-7027     TCGA-75-7031 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-7145     TCGA-78-7146     TCGA-78-7147     TCGA-78-7148 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-7149     TCGA-78-7150     TCGA-78-7152     TCGA-78-7153 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-7154     TCGA-78-7155     TCGA-78-7156     TCGA-78-7158 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-7159     TCGA-78-7160     TCGA-78-7161     TCGA-78-7162 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-7163     TCGA-78-7167     TCGA-78-7220     TCGA-78-7535 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-7536     TCGA-78-7537     TCGA-78-7539     TCGA-78-7542 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-78-8640     TCGA-78-8648     TCGA-78-8655     TCGA-80-5608 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-6851     TCGA-86-7711     TCGA-86-7714 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-86-7954     TCGA-86-8054     TCGA-86-8055     TCGA-86-8056 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-86-8073     TCGA-86-8074     TCGA-86-8281     TCGA-86-8358 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8669     TCGA-86-8673     TCGA-86-8674 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-86-A456     TCGA-91-6829     TCGA-91-6830     TCGA-91-6840 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-91-8499     TCGA-93-7347     TCGA-93-7348     TCGA-93-A4JN 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-93-A4JO     TCGA-95-7567     TCGA-95-7944     TCGA-95-A4VP 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-97-7546     TCGA-97-7553     TCGA-97-7554     TCGA-97-7941 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-97-8171     TCGA-97-8174     TCGA-97-8176     TCGA-97-8179 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-97-A4M0     TCGA-97-A4M1     TCGA-97-A4M5     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-A4AD 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-J2-A4AG     TCGA-L4-A4E5     TCGA-L4-A4E6     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-A4T9     TCGA-MP-A4TE 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-MP-A4TF     TCGA-MP-A4TH     TCGA-MP-A4TI     TCGA-MP-A4TK 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
    TCGA-MP-A5C7     TCGA-NJ-A4YG     TCGA-NJ-A4YI     TCGA-O1-A52J 
"RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" "RPL5 WILD-TYPE" 
                vv
clus              R0  R1  R2  RX
  RPL5 MUTATED     5   0   0   0
  RPL5 WILD-TYPE 307  12   4  25
D47V13, multiclass
    clus
vv   RPL5 MUTATED RPL5 WILD-TYPE
  R0            5            307
  R1            0             12
  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                        29   373
D47V14, multiclass
                                  clus
vv                                 RPL5 MUTATED RPL5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             29
  WHITE                                       5            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"
D47V15, binary
                cls
clus               0   1
  RPL5 MUTATED     0   6
  RPL5 WILD-TYPE   6 345
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPL5 MUTATED      0    6
  RPL5 WILD-TYPE    6  345
                        clus
vv                       RPL5 MUTATED RPL5 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            6            345
[1] 2 2
[1] FALSE

Clustering(48) Variable = STRA8 MUTATION ANALYSIS
D48V1, survival
                 sevent
clus2               0   1
  STRA8 MUTATED     6   2
  STRA8 WILD-TYPE 292 169
  STRA8 MUTATED STRA8 WILD-TYPE 
              8             461 
  STRA8 MUTATED STRA8 WILD-TYPE 
              2             169 
$`STRA8 MUTATED`
TCGA-05-4382 TCGA-44-7670 TCGA-05-4397 TCGA-44-5643 TCGA-44-5644 TCGA-73-4668 
       19.96        29.00        24.03        33.30        28.37        15.35 
TCGA-78-7536 TCGA-86-8054 
        8.02        37.74 

$`STRA8 WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       14.01         9.96         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       29.23         9.37        11.08        46.72        16.04        17.16 
TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 
       11.64        40.60        21.47        41.69        23.05        48.62 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        5.79         7.79         7.99        16.01        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       21.44         6.15        19.66        19.73        17.98        16.93 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       19.69        32.12        18.15        13.68        16.93        22.65 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       20.58        19.59        20.19        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       13.71        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        10.09        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       47.05        19.00         2.99        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        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-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 
       44.61         4.37        46.98        44.42        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 
       38.24        34.06        33.73        26.56        28.01        23.77 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       19.56        23.15        21.63        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        22.72        19.46         7.17        36.07        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         8.55        15.98        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 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-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 
       29.75        55.89        53.29        55.33        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47       101.72        15.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
        8.22         9.27        14.27        78.67         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       48.46        60.72        57.53        53.16        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05        12.16         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99        36.79        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       35.21        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       40.73        15.25        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
       70.26        31.30        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
       22.03         3.91        23.15        25.41        15.39        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 
       11.28        34.19        17.65        18.44        19.82        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       29.72        15.19        23.08         5.06        17.79        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       15.65        29.19        22.16        15.42        17.56        15.72 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
       14.47         0.36        13.74        20.28        17.72        19.96 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
       26.01        17.10        17.62        14.66         1.58        12.33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
       20.71        21.40         3.25         0.92        15.81        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 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-64-1679 
       13.61        39.25        40.96        29.92        56.81        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41        13.41        13.51        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 
       13.45         4.24        19.43         8.42         6.90        23.38 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 
       26.30         4.31        30.31         9.24         1.25        50.33 
TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 
       66.64        77.85        43.82        85.15        49.84        36.66 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
      108.66       100.57       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 
      104.19       238.29        88.14        26.53        31.20        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       26.01        39.35        10.55       232.18        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
      110.50        93.11        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 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        11.61 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-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-91-6840 TCGA-91-6847 TCGA-91-6848 
        1.97        10.19         2.60        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 
       17.46        23.61         1.08        19.00        41.82        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       12.39        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       21.60        20.58        21.44        19.76        20.84        18.67 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
       24.56        34.85        36.76         1.45        21.57        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 
       35.47        32.48        19.00        14.30        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        5.49        41.59        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       47.08         0.49         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           21.44 
[1] "8.0 - 37.7 (26.2)"  "0.0 - 238.3 (21.4)"
[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      121      130        45        63         68
                 vv
clus              STAGE IIIB STAGE IV
  STRA8 MUTATED            0        0
  STRA8 WILD-TYPE         11       24
D48V3, multiclass
            clus
vv           STRA8 MUTATED STRA8 WILD-TYPE
  STAGE I                0               4
  STAGE IA               0             121
  STAGE IB               2             130
  STAGE IIA              1              45
  STAGE IIB              3              63
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               0              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
  STRA8 MUTATED     1   7   0   0
  STRA8 WILD-TYPE 155 254  43  18
D48V4, multiclass
    clus
vv   STRA8 MUTATED STRA8 WILD-TYPE
  T1             1             155
  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 306  85    70
D48V5, multiclass
       clus
vv      STRA8 MUTATED STRA8 WILD-TYPE
  N0                2             306
  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 257 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STRA8 MUTATED      3    5
  STRA8 WILD-TYPE  257  216
        clus
vv       STRA8 MUTATED STRA8 WILD-TYPE
  FEMALE             3             257
  MALE               5             216
[1] 2 2
[1] FALSE
D48V8, binary
                 cls
clus                0   1
  STRA8 MUTATED     4   3
  STRA8 WILD-TYPE 380  52
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STRA8 MUTATED      4    3
  STRA8 WILD-TYPE  380   52
     clus
vv    STRA8 MUTATED STRA8 WILD-TYPE
  NO              4             380
  YES             3              52
[1] 2 2
[1] FALSE
D48V9, continuous
[1] "Remove cluster labels:" "STRA8 MUTATED"         
clus
  STRA8 MUTATED STRA8 WILD-TYPE 
              2             120 
     TCGA-44-6147      TCGA-44-A47F      TCGA-49-6742      TCGA-55-7573 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7914      TCGA-55-8205      TCGA-55-8511 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8621      TCGA-55-A491      TCGA-55-A492 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-64-1677      TCGA-73-4662      TCGA-73-7498      TCGA-93-8067 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-35-4122      TCGA-35-4123      TCGA-35-5375 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-44-3396      TCGA-44-3918      TCGA-44-4112      TCGA-44-6144 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-7660      TCGA-49-4486      TCGA-49-4494 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-49-4505      TCGA-49-4506      TCGA-49-4510      TCGA-49-6743 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-49-6744      TCGA-53-7624      TCGA-53-A4EZ      TCGA-55-5899 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7574      TCGA-55-7910      TCGA-55-7913 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-55-7995      TCGA-55-8089      TCGA-55-8096      TCGA-55-8208 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8512      TCGA-55-8513 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A494 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-62-8394      TCGA-62-8395      TCGA-62-8397      TCGA-62-8398 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O      TCGA-62-A46P 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U      TCGA-62-A46V 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471      TCGA-62-A472 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-64-1681      TCGA-64-5775      TCGA-64-5778      TCGA-69-7974 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-69-8254      TCGA-71-6725      TCGA-71-8520      TCGA-73-4659 
"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-73-7499      TCGA-75-5122      TCGA-83-5908      TCGA-86-6562 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-86-6851      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7953      TCGA-86-7954      TCGA-86-7955 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8073      TCGA-86-8074 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-86-8075      TCGA-86-8076      TCGA-86-8278      TCGA-86-8279 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-86-8280      TCGA-86-8281      TCGA-86-8358      TCGA-86-8359 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-A456 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6829      TCGA-91-6849 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-93-7347      TCGA-93-7348      TCGA-93-A4JN      TCGA-93-A4JO 
"STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" "STRA8 WILD-TYPE" 
     TCGA-95-7567      TCGA-99-7458      TCGA-MN-A4N4      TCGA-MN-A4N5 
"STRA8 WILD-TYPE" "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                         16                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  STRA8 MUTATED                                                    4
  STRA8 WILD-TYPE                                                292
                 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                                      16
  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"
D48V11, continuous
D48V12, continuous
                 vv
clus               R0  R1  R2  RX
  STRA8 MUTATED     5   0   0   0
  STRA8 WILD-TYPE 307  12   4  25
D48V13, multiclass
    clus
vv   STRA8 MUTATED STRA8 WILD-TYPE
  R0             5             307
  R1             0              12
  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                        29   374
D48V14, multiclass
                                  clus
vv                                 STRA8 MUTATED STRA8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              29
  WHITE                                        4             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"
D48V15, binary
                 cls
clus                0   1
  STRA8 MUTATED     1   4
  STRA8 WILD-TYPE   5 347
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STRA8 MUTATED      1    4
  STRA8 WILD-TYPE    5  347
                        clus
vv                       STRA8 MUTATED STRA8 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             4             347
[1] 2 2
[1] FALSE

Clustering(49) Variable = NLRP6 MUTATION ANALYSIS
D49V1, survival
                 sevent
clus2               0   1
  NLRP6 MUTATED     6   3
  NLRP6 WILD-TYPE 292 168
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              9             460 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              3             168 
$`NLRP6 MUTATED`
TCGA-97-A4M7 TCGA-05-4420 TCGA-44-7660 TCGA-55-6642 TCGA-55-7907 TCGA-55-8094 
       20.68        29.98        19.46        80.52        11.28        17.79 
TCGA-86-7714 TCGA-99-8025 TCGA-MP-A4SV 
       20.55        34.85        86.14 

$`NLRP6 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       17.29        16.54         2.86        15.68        15.65        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8192 
       18.18        17.92        20.19        20.52        17.75        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         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-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 
       23.18        32.45        61.28        16.44        22.72         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        48.46        60.72        57.53        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99        36.79        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 
       30.54        13.94        35.21        30.58        14.30         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
      107.21        70.26        31.30        28.67        20.02        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
       32.71        22.03         3.91        23.15        25.41        15.39 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 
       18.64        34.19        17.65        18.44        19.82        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 
       29.72        15.19        23.08         5.06        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       29.19        22.16        15.42        17.56        15.72        14.47 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36        13.74        20.28        17.72        19.96        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
       17.10        17.62        14.66         1.58        12.33        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 
       21.40         3.25         0.92        15.81        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-64-1679 TCGA-64-1681 
       39.25        40.96        29.92        56.81        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-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         4.41        13.41        13.51        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 
        4.24        19.43         8.42         6.90        23.38        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-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 
       66.64        77.85        43.82        85.15        49.84        36.66 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
      108.66       100.57       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      104.19       238.29        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
       53.33        26.01        39.35        10.55       232.18        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59       110.50        93.11        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 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 
       11.61        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-91-6840 TCGA-91-6847 
       41.36         1.97        10.19         2.60        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
        7.36         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       22.45        17.46        23.61         1.08        19.00        41.82 
TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 
       18.67        12.39        27.29         2.76        19.89        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        61.48        25.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       15.91        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       14.30        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
       18.67        24.56        36.76         1.45        21.57        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 
       35.47        32.48        19.00        14.30        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-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       41.59        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.49         0.43        19.82        59.11 

  NLRP6 MUTATED NLRP6 WILD-TYPE 
          11.28            0.00 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
          86.14          238.29 
  NLRP6 MUTATED NLRP6 WILD-TYPE 
          20.68           21.47 
[1] "11.3 - 86.1 (20.7)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.4"
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      120      127        45        66         68
                 vv
clus              STAGE IIIB STAGE IV
  NLRP6 MUTATED            0        1
  NLRP6 WILD-TYPE         11       23
D49V3, multiclass
            clus
vv           NLRP6 MUTATED NLRP6 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             120
  STAGE IB               5             127
  STAGE IIA              1              45
  STAGE IIB              0              66
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              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
  NLRP6 MUTATED     2   7   1   0
  NLRP6 WILD-TYPE 154 254  42  18
D49V4, multiclass
    clus
vv   NLRP6 MUTATED NLRP6 WILD-TYPE
  T1             2             154
  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 301  88    70
D49V5, multiclass
       clus
vv      NLRP6 MUTATED NLRP6 WILD-TYPE
  N0                7             301
  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 257 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      3    7
  NLRP6 WILD-TYPE  257  214
        clus
vv       NLRP6 MUTATED NLRP6 WILD-TYPE
  FEMALE             3             257
  MALE               7             214
[1] 2 2
[1] FALSE
D49V8, binary
                 cls
clus                0   1
  NLRP6 MUTATED     9   1
  NLRP6 WILD-TYPE 375  54
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      9    1
  NLRP6 WILD-TYPE  375   54
     clus
vv    NLRP6 MUTATED NLRP6 WILD-TYPE
  NO              9             375
  YES             1              54
[1] 2 2
[1] FALSE
D49V9, continuous
[1] "Remove cluster labels:" "NLRP6 MUTATED"         
clus
  NLRP6 MUTATED NLRP6 WILD-TYPE 
              2             120 
     TCGA-44-6147      TCGA-44-A47F      TCGA-49-6742      TCGA-55-7573 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7914      TCGA-55-8205      TCGA-55-8511 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8621      TCGA-55-A491      TCGA-55-A492 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-64-1677      TCGA-73-4662      TCGA-73-7498      TCGA-93-8067 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-35-4122      TCGA-35-4123      TCGA-35-5375 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-44-3396      TCGA-44-3918      TCGA-44-4112      TCGA-44-6144 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-44-6775      TCGA-49-4486      TCGA-49-4494      TCGA-49-4505 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-49-4506      TCGA-49-4510      TCGA-49-6743      TCGA-49-6744 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-53-7624      TCGA-53-A4EZ      TCGA-55-5899      TCGA-55-7283 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-55-7574      TCGA-55-7910      TCGA-55-7913      TCGA-55-7995 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-55-8089      TCGA-55-8096      TCGA-55-8208      TCGA-55-8507 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-55-8508      TCGA-55-8512      TCGA-55-8513      TCGA-55-8620 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A494      TCGA-62-8394 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-62-8395      TCGA-62-8397      TCGA-62-8398      TCGA-62-8399 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-62-8402      TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-62-A46S      TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-62-A470      TCGA-62-A471      TCGA-62-A472      TCGA-64-1681 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-64-5775      TCGA-64-5778      TCGA-69-7974      TCGA-69-8254 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-71-6725      TCGA-71-8520      TCGA-73-4659      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-73-7499      TCGA-75-5122      TCGA-83-5908      TCGA-86-6562 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-86-6851      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-86-7953      TCGA-86-7954      TCGA-86-7955      TCGA-86-8054 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-86-8055      TCGA-86-8056      TCGA-86-8073      TCGA-86-8074 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-86-8075      TCGA-86-8076      TCGA-86-8278      TCGA-86-8279 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-86-8280      TCGA-86-8281      TCGA-86-8358      TCGA-86-8359 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-A456 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6829      TCGA-91-6849 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-93-7347      TCGA-93-7348      TCGA-93-A4JN      TCGA-93-A4JO 
"NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" "NLRP6 WILD-TYPE" 
     TCGA-95-7567      TCGA-99-7458      TCGA-MN-A4N4      TCGA-MN-A4N5 
"NLRP6 WILD-TYPE" "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                         17                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NLRP6 MUTATED                                                    7
  NLRP6 WILD-TYPE                                                289
                 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                                      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"
D49V11, continuous
D49V12, continuous
                 vv
clus               R0  R1  R2  RX
  NLRP6 MUTATED     9   0   0   0
  NLRP6 WILD-TYPE 303  12   4  25
D49V13, multiclass
    clus
vv   NLRP6 MUTATED NLRP6 WILD-TYPE
  R0             9             303
  R1             0              12
  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                        28   373
D49V14, multiclass
                                  clus
vv                                 NLRP6 MUTATED NLRP6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              28
  WHITE                                        5             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"
D49V15, binary
                 cls
clus                0   1
  NLRP6 MUTATED     0   6
  NLRP6 WILD-TYPE   6 345
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP6 MUTATED      0    6
  NLRP6 WILD-TYPE    6  345
                        clus
vv                       NLRP6 MUTATED NLRP6 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             345
[1] 2 2
[1] FALSE

Clustering(50) Variable = FAM65C MUTATION ANALYSIS
D50V1, survival
                  sevent
clus2                0   1
  FAM65C MUTATED    10   3
  FAM65C WILD-TYPE 288 168
  FAM65C MUTATED FAM65C WILD-TYPE 
              13              456 
  FAM65C MUTATED FAM65C WILD-TYPE 
               3              168 
$`FAM65C MUTATED`
TCGA-44-7670 TCGA-93-8067 TCGA-44-7667 TCGA-44-A47A TCGA-49-4486 TCGA-55-8506 
       29.00         6.12        36.07        15.32        76.21         0.36 
TCGA-62-A46U TCGA-69-7978 TCGA-75-6214 TCGA-78-7163 TCGA-78-7220 TCGA-86-8073 
       67.96         4.41        36.66       238.29        26.53        24.33 
TCGA-97-7547 
       64.60 

$`FAM65C WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       18.31        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 
       85.32        13.71        16.18         1.45        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        10.09        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         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-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
        7.17        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 
        9.44        11.54        13.64        13.45        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-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 
       29.75        55.89        53.29        55.33        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47       101.72        15.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
        8.22         9.27        14.27        78.67         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       48.46        60.72        57.53        53.16        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05        12.16         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99        36.79        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       35.21        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       40.73        15.25        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
       70.26        31.30        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
       22.03         3.91        23.15        25.41        15.39        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 
       11.28        34.19        17.65        18.44        19.82        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       29.72        15.19        23.08         5.06        17.79        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       15.65        29.19        22.16        15.42        17.56        15.72 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
       14.47        13.74        20.28        17.72        19.96        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
       17.10        17.62        14.66         1.58        12.33        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 
       21.40         3.25         0.92        15.81        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-64-1679 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-69-7760 
       18.84        14.04        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 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 
       13.41        13.51        14.01        13.45         4.24        19.43 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        8.42         6.90        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       30.31         9.24         1.25        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       43.82        85.15        49.84       108.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 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-78-7167 TCGA-78-7535 
       64.90        22.92         9.57       104.19        88.14        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59       110.50        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.89        35.24        37.74         4.08         4.57         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       22.82        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60        11.61        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-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-91-6840 
       10.62        41.36         1.97        10.19         2.60        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45        17.46        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       41.82        18.67        12.39        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       42.25        63.52        61.48        25.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       15.91        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       14.30        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 
       18.08        35.47        32.48        19.00        14.30        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.85         5.49        41.59        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        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        47.08         0.49         0.43        19.82        59.11 

  FAM65C MUTATED FAM65C WILD-TYPE 
            0.36             0.00 
  FAM65C MUTATED FAM65C WILD-TYPE 
          238.29           232.18 
  FAM65C MUTATED FAM65C WILD-TYPE 
           29.00            21.42 
[1] "0.4 - 238.3 (29.0)" "0.0 - 232.2 (21.4)"
[1] "hr=" "2.4"
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      120      127        45        62         67
                  vv
clus               STAGE IIIB STAGE IV
  FAM65C MUTATED            0        0
  FAM65C WILD-TYPE         11       24
D50V3, multiclass
            clus
vv           FAM65C MUTATED FAM65C WILD-TYPE
  STAGE I                 0                4
  STAGE IA                1              120
  STAGE IB                5              127
  STAGE IIA               1               45
  STAGE IIB               4               62
  STAGE IIIA              3               67
  STAGE IIIB              0               11
  STAGE IV                0               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
  FAM65C MUTATED     2   9   3   0
  FAM65C WILD-TYPE 154 252  40  18
D50V4, multiclass
    clus
vv   FAM65C MUTATED FAM65C WILD-TYPE
  T1              2              154
  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 300  86    69
D50V5, multiclass
       clus
vv      FAM65C MUTATED FAM65C WILD-TYPE
  N0                 8              300
  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 251 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM65C MUTATED      9    5
  FAM65C WILD-TYPE  251  216
        clus
vv       FAM65C MUTATED FAM65C WILD-TYPE
  FEMALE              9              251
  MALE                5              216
[1] 2 2
[1] FALSE
D50V8, binary
                  cls
clus                 0   1
  FAM65C MUTATED    12   1
  FAM65C WILD-TYPE 372  54
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM65C MUTATED     12    1
  FAM65C WILD-TYPE  372   54
     clus
vv    FAM65C MUTATED FAM65C WILD-TYPE
  NO              12              372
  YES              1               54
[1] 2 2
[1] FALSE
D50V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FAM65C MUTATED                            0                                 3
  FAM65C WILD-TYPE                         17                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FAM65C MUTATED                                                    8
  FAM65C WILD-TYPE                                                288
                  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                                       17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                99
  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"
D50V11, continuous
D50V12, continuous
                  vv
clus                R0  R1  R2  RX
  FAM65C MUTATED     8   0   1   1
  FAM65C WILD-TYPE 304  12   3  24
D50V13, multiclass
    clus
vv   FAM65C MUTATED FAM65C WILD-TYPE
  R0              8              304
  R1              0               12
  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                        30   367
D50V14, multiclass
                                  clus
vv                                 FAM65C MUTATED FAM65C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1                6
  BLACK OR AFRICAN AMERICAN                     0               30
  WHITE                                        11              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"
D50V15, binary
                  cls
clus                 0   1
  FAM65C MUTATED     1   9
  FAM65C WILD-TYPE   5 342
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM65C MUTATED      1    9
  FAM65C WILD-TYPE    5  342
                        clus
vv                       FAM65C MUTATED FAM65C WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO              9              342
[1] 2 2
[1] FALSE

Clustering(51) Variable = WDR66 MUTATION ANALYSIS
D51V1, survival
                 sevent
clus2               0   1
  WDR66 MUTATED     9   5
  WDR66 WILD-TYPE 289 166
  WDR66 MUTATED WDR66 WILD-TYPE 
             14             455 
  WDR66 MUTATED WDR66 WILD-TYPE 
              5             166 
$`WDR66 MUTATED`
TCGA-55-A48X TCGA-05-4420 TCGA-35-5375 TCGA-53-7624 TCGA-62-8399 TCGA-67-3771 
       22.65        29.98         8.68        34.29        88.64        20.05 
TCGA-75-7027 TCGA-78-7155 TCGA-78-7536 TCGA-78-7539 TCGA-78-8662 TCGA-86-8056 
      100.57        38.50         8.02        26.01       110.50         4.57 
TCGA-99-8025 TCGA-O1-A52J 
       34.85        59.11 

$`WDR66 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       16.93        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 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-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 
       44.61         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-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        48.46        60.72        57.53        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 
        0.72        10.13        36.99        36.79        27.25        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       13.94        35.21        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
      107.21        70.26        31.30        28.67        20.02        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
       32.71        22.03         3.91        23.15        25.41        15.39 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       18.64        11.28        34.19        17.65        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       29.23        29.72        15.19        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.72        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       19.96        26.01        17.10        17.62        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       12.33        20.71        21.40         3.25         0.92        15.81 
TCGA-55-A4DG TCGA-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-64-1679 
       13.61        39.25        40.96        29.92        56.81        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3772 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-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        13.41        13.51        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 
        4.24        19.43         8.42         6.90        23.38        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-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 
       66.64        77.85        43.82        85.15        49.84        36.66 
TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
      108.66       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-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 
       88.14        26.53        31.20        53.33        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
      232.18        39.75        77.59        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 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        11.61        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-91-6840 
       10.62        41.36         1.97        10.19         2.60        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45        17.46        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       41.82        18.67        12.39        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       42.25        64.60        63.52        61.48        25.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59        15.91        18.67         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.84        18.67        24.56        36.76         1.45        21.57 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 
       18.08        35.47        32.48        19.00        14.30        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.85         5.49        41.59        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        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        1.64        47.08         0.49         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 
         32.135          21.400 
[1] "4.6 - 110.5 (32.1)" "0.0 - 238.3 (21.4)"
[1] "hr=" "1.6"
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      119      128        44        66         65
                 vv
clus              STAGE IIIB STAGE IV
  WDR66 MUTATED            0        1
  WDR66 WILD-TYPE         11       23
D51V3, multiclass
            clus
vv           WDR66 MUTATED WDR66 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             119
  STAGE IB               4             128
  STAGE IIA              2              44
  STAGE IIB              0              66
  STAGE IIIA             5              65
  STAGE IIIB             0              11
  STAGE IV               1              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
  WDR66 MUTATED     3   9   1   1
  WDR66 WILD-TYPE 153 252  42  17
D51V4, multiclass
    clus
vv   WDR66 MUTATED WDR66 WILD-TYPE
  T1             3             153
  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 299  88    68
D51V5, multiclass
       clus
vv      WDR66 MUTATED WDR66 WILD-TYPE
  N0                9             299
  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 252 215
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED      8    6
  WDR66 WILD-TYPE  252  215
        clus
vv       WDR66 MUTATED WDR66 WILD-TYPE
  FEMALE             8             252
  MALE               6             215
[1] 2 2
[1] FALSE
D51V8, binary
                 cls
clus                0   1
  WDR66 MUTATED     9   1
  WDR66 WILD-TYPE 375  54
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED      9    1
  WDR66 WILD-TYPE  375   54
     clus
vv    WDR66 MUTATED WDR66 WILD-TYPE
  NO              9             375
  YES             1              54
[1] 2 2
[1] FALSE
D51V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  WDR66 MUTATED                            0                                 3
  WDR66 WILD-TYPE                         17                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  WDR66 MUTATED                                                   10
  WDR66 WILD-TYPE                                                286
                 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                                      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                                   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 299  12   4  25
D51V13, multiclass
    clus
vv   WDR66 MUTATED WDR66 WILD-TYPE
  R0            13             299
  R1             0              12
  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                        28   369
D51V14, multiclass
                                  clus
vv                                 WDR66 MUTATED WDR66 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              28
  WHITE                                        9             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"
D51V15, binary
                 cls
clus                0   1
  WDR66 MUTATED     1   7
  WDR66 WILD-TYPE   5 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED      1    7
  WDR66 WILD-TYPE    5  344
                        clus
vv                       WDR66 MUTATED WDR66 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             7             344
[1] 2 2
[1] FALSE

Clustering(52) Variable = RIT1 MUTATION ANALYSIS
D52V1, survival
                sevent
clus2              0   1
  RIT1 MUTATED     5   3
  RIT1 WILD-TYPE 293 168
  RIT1 MUTATED RIT1 WILD-TYPE 
             8            461 
  RIT1 MUTATED RIT1 WILD-TYPE 
             3            168 
$`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        17.79        26.30        30.31 
TCGA-86-A4JF TCGA-J2-A4AE 
       24.23        35.47 

$`RIT1 WILD-TYPE`
TCGA-05-4382 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96         9.96         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       29.98        12.00        30.02        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       25.02        24.00         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       37.71        49.05        44.61         4.37        46.98        44.42 
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-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 
       21.63        23.18        32.45        61.28        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 TCGA-49-6744 
       32.84         8.81        29.46        29.75        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        48.46        60.72        57.53        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99        36.79        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       30.54        13.94        35.21        30.58        14.30        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        5.62        42.51        40.73        15.25        46.03        53.65 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26        31.30        28.67        20.02 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       27.09        32.71        22.03         3.91        23.15        25.41 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 
       15.39        18.64        11.28        34.19        17.65        18.44 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 
       19.82        29.23        29.72        15.19        23.08         5.06 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.72        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       19.96        26.01        17.10        17.62        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       12.33        20.71        21.40         3.25         0.92        15.81 
TCGA-55-A4DG TCGA-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-64-1679 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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        19.43         8.42         6.90 
TCGA-73-4659 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 
       23.38        15.35         4.31         9.24         1.25        50.33 
TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 
       66.64        77.85        43.82        85.15        49.84        36.66 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
      108.66       100.57       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      104.19       238.29        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
       53.33        26.01        39.35        10.55       232.18        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59       110.50        93.11        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        38.04        20.55        32.78        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       35.24        37.74         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       22.82        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60        11.61        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-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-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
        7.36         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       22.45        17.46        23.61         1.08        19.00        41.82 
TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 
       18.67        12.39        27.29         2.76        19.89        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        61.48        25.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       15.91        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       14.30        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 
       18.08        32.48        19.00        14.30        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        5.49        41.59        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       47.08         0.49         0.43        19.82        59.11 

  RIT1 MUTATED RIT1 WILD-TYPE 
         14.01           0.00 
  RIT1 MUTATED RIT1 WILD-TYPE 
         55.89         238.29 
  RIT1 MUTATED RIT1 WILD-TYPE 
        25.265         21.440 
[1] "14.0 - 55.9 (25.3)" "0.0 - 238.3 (21.4)"
[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      119      132        46        64         68
                vv
clus             STAGE IIIB STAGE IV
  RIT1 MUTATED            0        2
  RIT1 WILD-TYPE         11       22
D52V3, multiclass
            clus
vv           RIT1 MUTATED RIT1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              2            119
  STAGE IB              0            132
  STAGE IIA             0             46
  STAGE IIB             2             64
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              2             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
  RIT1 MUTATED     3   3   2   0
  RIT1 WILD-TYPE 153 258  41  18
D52V4, multiclass
    clus
vv   RIT1 MUTATED RIT1 WILD-TYPE
  T1            3            153
  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 303  87    71
D52V5, multiclass
       clus
vv      RIT1 MUTATED RIT1 WILD-TYPE
  N0               5            303
  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 256 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIT1 MUTATED      4    4
  RIT1 WILD-TYPE  256  217
        clus
vv       RIT1 MUTATED RIT1 WILD-TYPE
  FEMALE            4            256
  MALE              4            217
[1] 2 2
[1] FALSE
D52V8, binary
                cls
clus               0   1
  RIT1 MUTATED     5   3
  RIT1 WILD-TYPE 379  52
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIT1 MUTATED      5    3
  RIT1 WILD-TYPE  379   52
     clus
vv    RIT1 MUTATED RIT1 WILD-TYPE
  NO             5            379
  YES            3             52
[1] 2 2
[1] FALSE
D52V9, continuous
[1] "Remove cluster labels:" "RIT1 MUTATED"          
clus
  RIT1 MUTATED RIT1 WILD-TYPE 
             2            120 
    TCGA-44-6147     TCGA-44-A47F     TCGA-49-6742     TCGA-55-7573 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-55-7725     TCGA-55-7914     TCGA-55-8205     TCGA-55-8511 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8621     TCGA-55-A491     TCGA-55-A492 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-64-1677     TCGA-73-4662     TCGA-73-7498     TCGA-93-8067 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-35-4122     TCGA-35-4123     TCGA-35-5375 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-44-3396     TCGA-44-3918     TCGA-44-4112     TCGA-44-6144 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-44-6775     TCGA-44-7660     TCGA-49-4486     TCGA-49-4494 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-49-4505     TCGA-49-4506     TCGA-49-4510     TCGA-49-6743 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-49-6744     TCGA-53-7624     TCGA-53-A4EZ     TCGA-55-5899 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-55-7283     TCGA-55-7574     TCGA-55-7910     TCGA-55-7913 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-55-7995     TCGA-55-8089     TCGA-55-8096     TCGA-55-8208 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-55-8507     TCGA-55-8508     TCGA-55-8512     TCGA-55-8513 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-55-8620     TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A494 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-62-8394     TCGA-62-8395     TCGA-62-8397     TCGA-62-8398 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-62-8399     TCGA-62-8402     TCGA-62-A46O     TCGA-62-A46P 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-62-A46R     TCGA-62-A46S     TCGA-62-A46U     TCGA-62-A46V 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-62-A46Y     TCGA-62-A470     TCGA-62-A471     TCGA-62-A472 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-64-1681     TCGA-64-5775     TCGA-64-5778     TCGA-69-7974 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-69-8254     TCGA-71-6725     TCGA-71-8520     TCGA-73-4659 
"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-73-7499     TCGA-75-5122     TCGA-83-5908     TCGA-86-6562 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-86-6851     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7953     TCGA-86-7954     TCGA-86-7955 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-86-8054     TCGA-86-8055     TCGA-86-8056     TCGA-86-8073 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-86-8074     TCGA-86-8075     TCGA-86-8076     TCGA-86-8278 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-86-8279     TCGA-86-8280     TCGA-86-8281     TCGA-86-8358 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-86-A456     TCGA-86-A4P7     TCGA-91-6829     TCGA-91-6849 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-93-7347     TCGA-93-7348     TCGA-93-A4JN     TCGA-93-A4JO 
"RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" "RIT1 WILD-TYPE" 
    TCGA-95-7567     TCGA-99-7458     TCGA-MN-A4N4     TCGA-MN-A4N5 
"RIT1 WILD-TYPE" "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                         17                               101
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RIT1 MUTATED                                                    6
  RIT1 WILD-TYPE                                                290
                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                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             101
  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"
D52V11, continuous
D52V12, continuous
                vv
clus              R0  R1  R2  RX
  RIT1 MUTATED     5   0   0   2
  RIT1 WILD-TYPE 307  12   4  23
D52V13, multiclass
    clus
vv   RIT1 MUTATED RIT1 WILD-TYPE
  R0            5            307
  R1            0             12
  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                        30   371
D52V14, multiclass
                                  clus
vv                                 RIT1 MUTATED RIT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             30
  WHITE                                       7            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"
D52V15, binary
                cls
clus               0   1
  RIT1 MUTATED     0   5
  RIT1 WILD-TYPE   6 346
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIT1 MUTATED      0    5
  RIT1 WILD-TYPE    6  346
                        clus
vv                       RIT1 MUTATED RIT1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            5            346
[1] 2 2
[1] FALSE

Clustering(53) Variable = TGFBR3 MUTATION ANALYSIS
D53V1, survival
                  sevent
clus2                0   1
  TGFBR3 MUTATED     9   5
  TGFBR3 WILD-TYPE 289 166
  TGFBR3 MUTATED TGFBR3 WILD-TYPE 
              14              455 
  TGFBR3 MUTATED TGFBR3 WILD-TYPE 
               5              166 
$`TGFBR3 MUTATED`
TCGA-55-8205 TCGA-95-7043 TCGA-L9-A444 TCGA-44-2656 TCGA-44-7662 TCGA-55-8089 
       19.69        16.54        10.09        46.98         7.17        23.08 
TCGA-55-8615 TCGA-62-A46O TCGA-78-7220 TCGA-78-7536 TCGA-83-5908 TCGA-99-7458 
       14.66        47.80        26.53         8.02        27.09        24.56 
TCGA-99-8025 TCGA-L4-A4E5 
       34.85        19.00 

$`TGFBR3 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       17.98        16.93        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        6.35        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       47.05        19.00         2.99        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-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-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       44.61         4.37        44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       23.77        19.56        23.15        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 
       61.28        16.44        22.72        19.46        36.07        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         8.55        15.98        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 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-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 
       29.75        55.89        53.29        55.33        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47       101.72        15.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
        8.22         9.27        14.27        78.67         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       48.46        60.72        57.53        53.16        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05        12.16         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99        36.79        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       35.21        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       40.73        15.25        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
       70.26        31.30        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
       22.03         3.91        23.15        25.41        15.39        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 
       11.28        34.19        17.65        18.44        19.82        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       29.72        15.19         5.06        17.79        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       29.19        22.16        15.42        17.56        15.72        14.47 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36        13.74        20.28        17.72        19.96        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.10        17.62         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        3.25         0.92        15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       29.92        56.81        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-69-7760 TCGA-69-7761 
       14.04        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
       13.41        13.51        14.01        13.45         4.24        19.43 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        8.42         6.90        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       30.31         9.24         1.25        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7167 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       88.14        31.20        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-86-6562 
      232.18        39.75        77.59       110.50        93.11        12.36 
TCGA-86-6851 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        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.18        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
       19.00        41.82        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       15.39        16.41        14.30        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       19.76        20.84        18.67        36.76         1.45        21.57 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 
       18.08        35.47        32.48        14.30        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        5.49        41.59        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       47.08         0.49         0.43        19.82        59.11 

  TGFBR3 MUTATED TGFBR3 WILD-TYPE 
            7.17             0.00 
  TGFBR3 MUTATED TGFBR3 WILD-TYPE 
           47.80           238.29 
  TGFBR3 MUTATED TGFBR3 WILD-TYPE 
          21.385           21.470 
[1] "7.2 - 47.8 (21.4)"  "0.0 - 238.3 (21.5)"
[1] "hr=" "1.3"
D53V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  TGFBR3 MUTATED         1        4        3         1         0          5
  TGFBR3 WILD-TYPE       3      117      129        45        66         65
                  vv
clus               STAGE IIIB STAGE IV
  TGFBR3 MUTATED            0        0
  TGFBR3 WILD-TYPE         11       24
D53V3, multiclass
            clus
vv           TGFBR3 MUTATED TGFBR3 WILD-TYPE
  STAGE I                 1                3
  STAGE IA                4              117
  STAGE IB                3              129
  STAGE IIA               1               45
  STAGE IIB               0               66
  STAGE IIIA              5               65
  STAGE IIIB              0               11
  STAGE IV                0               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
  TGFBR3 MUTATED     5   6   2   1
  TGFBR3 WILD-TYPE 151 255  41  17
D53V4, multiclass
    clus
vv   TGFBR3 MUTATED TGFBR3 WILD-TYPE
  T1              5              151
  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 298  89    68
D53V5, multiclass
       clus
vv      TGFBR3 MUTATED TGFBR3 WILD-TYPE
  N0                10              298
  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 251 216
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR3 MUTATED      9    5
  TGFBR3 WILD-TYPE  251  216
        clus
vv       TGFBR3 MUTATED TGFBR3 WILD-TYPE
  FEMALE              9              251
  MALE                5              216
[1] 2 2
[1] FALSE
D53V8, binary
                  cls
clus                 0   1
  TGFBR3 MUTATED    12   2
  TGFBR3 WILD-TYPE 372  53
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR3 MUTATED     12    2
  TGFBR3 WILD-TYPE  372   53
     clus
vv    TGFBR3 MUTATED TGFBR3 WILD-TYPE
  NO              12              372
  YES              2               53
[1] 2 2
[1] FALSE
D53V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TGFBR3 MUTATED                            0                                 2
  TGFBR3 WILD-TYPE                         17                               100
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TGFBR3 MUTATED                                                   11
  TGFBR3 WILD-TYPE                                                285
                  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                                       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"
D53V11, continuous
D53V12, continuous
                  vv
clus                R0  R1  R2  RX
  TGFBR3 MUTATED    11   0   0   0
  TGFBR3 WILD-TYPE 301  12   4  25
D53V13, multiclass
    clus
vv   TGFBR3 MUTATED TGFBR3 WILD-TYPE
  R0             11              301
  R1              0               12
  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                        29   365
D53V14, multiclass
                                  clus
vv                                 TGFBR3 MUTATED TGFBR3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               29
  WHITE                                        13              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"
D53V15, binary
                  cls
clus                 0   1
  TGFBR3 MUTATED     0  12
  TGFBR3 WILD-TYPE   6 339
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR3 MUTATED      0   12
  TGFBR3 WILD-TYPE    6  339
                        clus
vv                       TGFBR3 MUTATED TGFBR3 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             12              339
[1] 2 2
[1] FALSE

Clustering(54) Variable = CXCR7 MUTATION ANALYSIS
D54V1, survival
                 sevent
clus2               0   1
  CXCR7 MUTATED     6   3
  CXCR7 WILD-TYPE 292 168
  CXCR7 MUTATED CXCR7 WILD-TYPE 
              9             460 
  CXCR7 MUTATED CXCR7 WILD-TYPE 
              3             168 
$`CXCR7 MUTATED`
TCGA-44-8119 TCGA-91-7771 TCGA-55-8089 TCGA-55-8301 TCGA-67-4679 TCGA-75-5125 
        9.37        16.18        23.08        17.56        14.73        66.64 
TCGA-78-7155 TCGA-91-6831 TCGA-95-7039 
       38.50        10.19        41.82 

$`CXCR7 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       18.31        29.00        29.23        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       85.32        13.71         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        10.09        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         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-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       55.33        22.26        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       53.16        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 
       34.29        30.54        13.94        35.21        30.58        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       80.52         5.62        42.51        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       53.65         3.88        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26        31.30        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       20.02        27.09        32.71        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       25.41        15.39        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 
       18.44        19.82        29.23        29.72        15.19         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       17.79        23.64        15.65        29.19        22.16        15.42 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.72        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       19.96        26.01        17.10        17.62        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       12.33        20.71        21.40         3.25         0.92        15.81 
TCGA-55-A4DG TCGA-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-64-1679 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-67-6215 
       51.25        28.47        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41        13.41        13.51        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 
       13.45         4.24        19.43         8.42         6.90        23.38 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7499 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 
       50.33        77.85        43.82        85.15        49.84        36.66 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
      108.66       100.57       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      238.29        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       26.01        39.35        10.55       232.18        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
      110.50        93.11        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 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 
       11.61        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-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       41.36         1.97         2.60        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7567 TCGA-95-7944 
       17.46        23.61         1.08        19.00        18.67        12.39 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       27.29         2.76        19.89        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       61.48        25.48        18.54         0.59        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       20.58        21.44        19.76        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE 
       34.85        36.76         1.45        21.57        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       32.48        19.00        14.30        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       41.59        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.49         0.43        19.82        59.11 

  CXCR7 MUTATED CXCR7 WILD-TYPE 
           9.37            0.00 
  CXCR7 MUTATED CXCR7 WILD-TYPE 
          66.64          238.29 
  CXCR7 MUTATED CXCR7 WILD-TYPE 
          17.56           21.47 
[1] "9.4 - 66.6 (17.6)"  "0.0 - 238.3 (21.5)"
[1] "hr=" "1"  
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      120      128        46        62         70
                 vv
clus              STAGE IIIB STAGE IV
  CXCR7 MUTATED            0        0
  CXCR7 WILD-TYPE         11       24
D54V3, multiclass
            clus
vv           CXCR7 MUTATED CXCR7 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             120
  STAGE IB               4             128
  STAGE IIA              0              46
  STAGE IIB              4              62
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              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
  CXCR7 MUTATED     1   5   4   0
  CXCR7 WILD-TYPE 155 256  39  18
D54V4, multiclass
    clus
vv   CXCR7 MUTATED CXCR7 WILD-TYPE
  T1             1             155
  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 299  88    72
D54V5, multiclass
       clus
vv      CXCR7 MUTATED CXCR7 WILD-TYPE
  N0                9             299
  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 259 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCR7 MUTATED      1    9
  CXCR7 WILD-TYPE  259  212
        clus
vv       CXCR7 MUTATED CXCR7 WILD-TYPE
  FEMALE             1             259
  MALE               9             212
[1] 2 2
[1] FALSE
D54V8, binary
                 cls
clus                0   1
  CXCR7 MUTATED     7   0
  CXCR7 WILD-TYPE 377  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCR7 MUTATED      7    0
  CXCR7 WILD-TYPE  377   55
     clus
vv    CXCR7 MUTATED CXCR7 WILD-TYPE
  NO              7             377
  YES             0              55
[1] 2 2
[1] FALSE
D54V9, continuous
[1] "Remove cluster labels:" "CXCR7 MUTATED"         
clus
  CXCR7 MUTATED CXCR7 WILD-TYPE 
              1             121 
     TCGA-44-6147      TCGA-44-A47F      TCGA-49-6742      TCGA-55-7573 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7914      TCGA-55-8205      TCGA-55-8511 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8621      TCGA-55-A491      TCGA-55-A492 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-64-1677      TCGA-73-4662      TCGA-73-7498      TCGA-93-8067 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-35-4122      TCGA-35-4123      TCGA-35-5375 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-44-3396      TCGA-44-3918      TCGA-44-4112      TCGA-44-6144 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-7660      TCGA-49-4486      TCGA-49-4494 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-49-4505      TCGA-49-4506      TCGA-49-4510      TCGA-49-6743 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-49-6744      TCGA-53-7624      TCGA-53-A4EZ      TCGA-55-5899 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7574      TCGA-55-7910      TCGA-55-7913 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-55-7995      TCGA-55-8096      TCGA-55-8208      TCGA-55-8507 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-55-8508      TCGA-55-8512      TCGA-55-8513      TCGA-55-8620 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A494      TCGA-62-8394 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-62-8395      TCGA-62-8397      TCGA-62-8398      TCGA-62-8399 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-62-8402      TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-62-A46S      TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-62-A470      TCGA-62-A471      TCGA-62-A472      TCGA-64-1681 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-64-5775      TCGA-64-5778      TCGA-69-7974      TCGA-69-8254 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-71-6725      TCGA-71-8520      TCGA-73-4659      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-73-7499      TCGA-75-5122      TCGA-83-5908      TCGA-86-6562 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-86-6851      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7953      TCGA-86-7954      TCGA-86-7955 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-86-8054      TCGA-86-8055      TCGA-86-8056      TCGA-86-8073 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8075      TCGA-86-8076      TCGA-86-8278 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8280      TCGA-86-8281      TCGA-86-8358 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8668      TCGA-86-8669      TCGA-86-8671 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-86-A456      TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6829 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-91-6849      TCGA-93-7347      TCGA-93-7348      TCGA-93-A4JN 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-93-A4JO      TCGA-95-7567      TCGA-99-7458      TCGA-MN-A4N4 
"CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" "CXCR7 WILD-TYPE" 
     TCGA-MN-A4N5 
"CXCR7 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CXCR7 MUTATED                            0                                 1
  CXCR7 WILD-TYPE                         17                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CXCR7 MUTATED                                                    9
  CXCR7 WILD-TYPE                                                287
                 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                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  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"
D54V11, continuous
D54V12, continuous
                 vv
clus               R0  R1  R2  RX
  CXCR7 MUTATED     5   0   0   1
  CXCR7 WILD-TYPE 307  12   4  24
D54V13, multiclass
    clus
vv   CXCR7 MUTATED CXCR7 WILD-TYPE
  R0             5             307
  R1             0              12
  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                        30   370
D54V14, multiclass
                                  clus
vv                                 CXCR7 MUTATED CXCR7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              30
  WHITE                                        8             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"
D54V15, binary
                 cls
clus                0   1
  CXCR7 MUTATED     0   7
  CXCR7 WILD-TYPE   6 344
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCR7 MUTATED      0    7
  CXCR7 WILD-TYPE    6  344
                        clus
vv                       CXCR7 MUTATED CXCR7 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             7             344
[1] 2 2
[1] FALSE

Clustering(55) Variable = GAN MUTATION ANALYSIS
D55V1, survival
               sevent
clus2             0   1
  GAN MUTATED     3   7
  GAN WILD-TYPE 295 164
  GAN MUTATED GAN WILD-TYPE 
           10           459 
  GAN MUTATED GAN WILD-TYPE 
            7           164 
$`GAN MUTATED`
TCGA-05-4396 TCGA-05-4249 TCGA-44-3918 TCGA-49-4494 TCGA-53-7626 TCGA-55-7574 
        9.96        50.07        34.06        35.54        30.54        32.71 
TCGA-62-A46O TCGA-78-7150 TCGA-91-6830 TCGA-MP-A4TK 
       47.80        21.90         1.97        19.13 

$`GAN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        2.43        10.09         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         4.37        46.98        44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.11        28.57        12.66        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 
       29.46        29.75        55.89        53.29        55.33        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       49.28         8.22         9.27        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
        3.91        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 
       10.13        36.99        36.79        27.25        34.29        13.94 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       35.21        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       40.73        15.25        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7576 
       70.26        31.30        28.67        20.02        27.09        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        3.91        23.15        25.41        15.39        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       34.19        17.65        18.44        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       15.19        23.08         5.06        17.79        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       29.19        22.16        15.42        17.56        15.72        14.47 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36        13.74        20.28        17.72        19.96        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
       17.10        17.62        14.66         1.58        12.33        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 
       21.40         3.25         0.92        15.81        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-69-7760 
       18.84        14.04        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41        13.41        13.51        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       19.43         8.42         6.90        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 
        4.31        30.31         9.24         1.25        50.33        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       77.85        43.82        85.15        49.84        36.66       108.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
      100.57       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
      129.53        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 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        11.61 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-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-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        12.23        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
       23.61         1.08        19.00        41.82        18.67        12.39 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       27.29         2.76        19.89        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       61.48        25.48        18.54         0.59        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       20.58        21.44        19.76        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE 
       34.85        36.76         1.45        21.57        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       32.48        19.00        14.30        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
       41.59        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        74.33         0.13         1.64        47.08         0.49 
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 
       31.625        21.440 
[1] "2.0 - 50.1 (31.6)"  "0.0 - 238.3 (21.4)"
[1] "hr=" "1.9"
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      120      129        44        64         69
               vv
clus            STAGE IIIB STAGE IV
  GAN MUTATED            1        0
  GAN WILD-TYPE         10       24
D55V3, multiclass
            clus
vv           GAN MUTATED GAN WILD-TYPE
  STAGE I              0             4
  STAGE IA             1           120
  STAGE IB             3           129
  STAGE IIA            2            44
  STAGE IIB            2            64
  STAGE IIIA           1            69
  STAGE IIIB           1            10
  STAGE IV             0            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
  GAN MUTATED     3   5   1   1
  GAN WILD-TYPE 153 256  42  17
D55V4, multiclass
    clus
vv   GAN MUTATED GAN WILD-TYPE
  T1           3           153
  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 304  84    71
D55V5, multiclass
       clus
vv      GAN MUTATED GAN WILD-TYPE
  N0              4           304
  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 254 217
[1] "tbl2"
               cls
clus            [,1] [,2]
  GAN MUTATED      6    4
  GAN WILD-TYPE  254  217
        clus
vv       GAN MUTATED GAN WILD-TYPE
  FEMALE           6           254
  MALE             4           217
[1] 2 2
[1] FALSE
D55V8, binary
               cls
clus              0   1
  GAN MUTATED     7   1
  GAN WILD-TYPE 377  54
[1] "tbl2"
               cls
clus            [,1] [,2]
  GAN MUTATED      7    1
  GAN WILD-TYPE  377   54
     clus
vv    GAN MUTATED GAN WILD-TYPE
  NO            7           377
  YES           1            54
[1] 2 2
[1] FALSE
D55V9, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  GAN MUTATED                            0                                 1
  GAN WILD-TYPE                         17                               101
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  GAN MUTATED                                                    9
  GAN WILD-TYPE                                                287
               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            17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            1           101
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)           9           287
  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 304  11   4  25
D55V13, multiclass
    clus
vv   GAN MUTATED GAN WILD-TYPE
  R0           8           304
  R1           1            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
  GAN MUTATED                                  0     0
  GAN WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  GAN MUTATED                           0     7
  GAN WILD-TYPE                        30   371
D55V14, multiclass
                                  clus
vv                                 GAN MUTATED GAN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             7
  BLACK OR AFRICAN AMERICAN                  0            30
  WHITE                                      7           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"
D55V15, binary
               cls
clus              0   1
  GAN MUTATED     0   6
  GAN WILD-TYPE   6 345
[1] "tbl2"
               cls
clus            [,1] [,2]
  GAN MUTATED      0    6
  GAN WILD-TYPE    6  345
                        clus
vv                       GAN MUTATED GAN WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO           6           345
[1] 2 2
[1] FALSE

Clustering(56) Variable = TMEM49 MUTATION ANALYSIS
D56V1, survival
                  sevent
clus2                0   1
  TMEM49 MUTATED     2   3
  TMEM49 WILD-TYPE 296 168
  TMEM49 MUTATED TMEM49 WILD-TYPE 
               5              464 
  TMEM49 MUTATED TMEM49 WILD-TYPE 
               3              168 
$`TMEM49 MUTATED`
TCGA-50-5933 TCGA-50-8459 TCGA-53-7626 TCGA-69-7974 TCGA-MP-A4T4 
       78.67        36.79        30.54         6.05        86.04 

$`TMEM49 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       17.29        16.54         2.86        15.68        15.65        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       18.18        17.92        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 
       24.30        23.80         6.35        10.09        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 
       31.23         2.43        10.09        50.07         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       37.02         0.00        24.03        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        24.00         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-38-4632 TCGA-38-A44F TCGA-44-2656 
      120.79        37.71        49.05        44.61         4.37        46.98 
TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        23.18        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       22.72        19.46         7.17        36.07        18.87        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       12.66         8.55        15.98        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       35.54        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       55.89        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 
      101.72        15.72        60.16        47.41        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
        9.27        14.27         8.45        15.12        48.46        60.72 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       57.53        53.16        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8460 
       12.16         6.21         0.72        10.13        36.99        27.25 
TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       34.29        13.94        35.21        30.58        14.30        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        5.62        42.51        40.73        15.25        46.03        53.65 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26        31.30        28.67        20.02 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       27.09        32.71        22.03         3.91        23.15        25.41 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 
       15.39        18.64        11.28        34.19        17.65        18.44 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 
       19.82        29.23        29.72        15.19        23.08         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       17.79        23.64        15.65        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       17.56        15.72        14.47         0.36        13.74        20.28 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
        1.58        12.33        20.71        21.40         3.25         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       56.81        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-69-7760 TCGA-69-7761 TCGA-69-7763 
       14.73         5.72         4.64         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
       13.61         5.42         7.56         4.41        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        19.43         8.42         6.90 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       23.38        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
        1.25        50.33        66.64        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       49.84        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
       22.92         9.57       104.19       238.29        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
        1.08        19.00        41.82        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       25.48        18.54         0.59        15.91        18.67         5.39 
TCGA-97-8175 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-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       36.76         1.45        21.57        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       19.00        14.30        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE 
       49.35        37.35        58.85         5.49        41.59        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 
       74.33         0.13         1.64        47.08         0.49         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 
           36.79            21.44 
[1] "6.0 - 86.0 (36.8)"  "0.0 - 238.3 (21.4)"
[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      121      132        45        64         69
                  vv
clus               STAGE IIIB STAGE IV
  TMEM49 MUTATED            1        0
  TMEM49 WILD-TYPE         10       24
D56V3, multiclass
            clus
vv           TMEM49 MUTATED TMEM49 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                0              121
  STAGE IB                0              132
  STAGE IIA               1               45
  STAGE IIB               2               64
  STAGE IIIA              1               69
  STAGE IIIB              1               10
  STAGE IV                0               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
  TMEM49 MUTATED     1   2   1   1
  TMEM49 WILD-TYPE 155 259  42  17
D56V4, multiclass
    clus
vv   TMEM49 MUTATED TMEM49 WILD-TYPE
  T1              1              155
  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 307  87    70
D56V5, multiclass
       clus
vv      TMEM49 MUTATED TMEM49 WILD-TYPE
  N0                 1              307
  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 257 219
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM49 MUTATED      3    2
  TMEM49 WILD-TYPE  257  219
        clus
vv       TMEM49 MUTATED TMEM49 WILD-TYPE
  FEMALE              3              257
  MALE                2              219
[1] 2 2
[1] FALSE
D56V8, binary
                  cls
clus                 0   1
  TMEM49 MUTATED     3   2
  TMEM49 WILD-TYPE 381  53
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM49 MUTATED      3    2
  TMEM49 WILD-TYPE  381   53
     clus
vv    TMEM49 MUTATED TMEM49 WILD-TYPE
  NO               3              381
  YES              2               53
[1] 2 2
[1] FALSE
D56V9, continuous
[1] "Remove cluster labels:" "TMEM49 MUTATED"        
clus
  TMEM49 MUTATED TMEM49 WILD-TYPE 
               1              121 
      TCGA-44-6147       TCGA-44-A47F       TCGA-49-6742       TCGA-55-7573 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-7725       TCGA-55-7914       TCGA-55-8205       TCGA-55-8511 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-8619       TCGA-55-8621       TCGA-55-A491       TCGA-55-A492 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-64-1677       TCGA-73-4662       TCGA-73-7498       TCGA-93-8067 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-35-4122       TCGA-35-4123       TCGA-35-5375 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-44-3396       TCGA-44-3918       TCGA-44-4112       TCGA-44-6144 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-44-6775       TCGA-44-7660       TCGA-49-4486       TCGA-49-4494 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-49-4505       TCGA-49-4506       TCGA-49-4510       TCGA-49-6743 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-49-6744       TCGA-53-7624       TCGA-53-A4EZ       TCGA-55-5899 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7574       TCGA-55-7910       TCGA-55-7913 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-7995       TCGA-55-8089       TCGA-55-8096       TCGA-55-8208 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-8507       TCGA-55-8508       TCGA-55-8512       TCGA-55-8513 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-8620       TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A494 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-62-8394       TCGA-62-8395       TCGA-62-8397       TCGA-62-8398 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O       TCGA-62-A46P 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U       TCGA-62-A46V 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471       TCGA-62-A472 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-64-1681       TCGA-64-5775       TCGA-64-5778       TCGA-69-8254 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-71-6725       TCGA-71-8520       TCGA-73-4659       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-73-7499       TCGA-75-5122       TCGA-83-5908       TCGA-86-6562 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-6851       TCGA-86-7701       TCGA-86-7711       TCGA-86-7713 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-7714       TCGA-86-7953       TCGA-86-7954       TCGA-86-7955 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-8054       TCGA-86-8055       TCGA-86-8056       TCGA-86-8073 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-8074       TCGA-86-8075       TCGA-86-8076       TCGA-86-8278 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-8279       TCGA-86-8280       TCGA-86-8281       TCGA-86-8358 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-A456       TCGA-86-A4JF       TCGA-86-A4P7       TCGA-91-6829 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-91-6849       TCGA-93-7347       TCGA-93-7348       TCGA-93-A4JN 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-93-A4JO       TCGA-95-7567       TCGA-99-7458       TCGA-MN-A4N4 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-MN-A4N5 
"TMEM49 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TMEM49 MUTATED                            0                                 1
  TMEM49 WILD-TYPE                         17                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TMEM49 MUTATED                                                    3
  TMEM49 WILD-TYPE                                                293
                  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                                       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                                      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 310  12   4  25
D56V13, multiclass
[1] "Remove cluster labels:" "TMEM49 MUTATED"        
clus
  TMEM49 MUTATED TMEM49 WILD-TYPE 
               2              351 
      TCGA-05-4382       TCGA-05-4384       TCGA-05-4396       TCGA-05-4402 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-05-4405       TCGA-05-4410       TCGA-05-4418       TCGA-05-4427 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-05-4434       TCGA-05-5420       TCGA-38-4629       TCGA-38-4630 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-38-4631       TCGA-38-6178       TCGA-38-7271       TCGA-44-2661 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-49-4501       TCGA-49-6742       TCGA-49-6761       TCGA-50-6597 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-1592       TCGA-55-7284       TCGA-55-7724       TCGA-55-7725 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-7726       TCGA-55-7914       TCGA-55-8090       TCGA-55-8091 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-8203       TCGA-55-8204       TCGA-55-8205       TCGA-55-8207 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-8511       TCGA-55-8619       TCGA-55-8621       TCGA-55-A48X 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-A491       TCGA-55-A492       TCGA-55-A4DF       TCGA-64-1677 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-67-6217       TCGA-73-4658       TCGA-73-4662       TCGA-73-7498 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-78-7166       TCGA-78-7633       TCGA-78-8660       TCGA-80-5607 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-80-5611       TCGA-93-8067       TCGA-93-A4JQ       TCGA-95-7562 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-95-7947       TCGA-95-7948       TCGA-95-A4VK       TCGA-95-A4VN 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-97-A4M2       TCGA-97-A4M7       TCGA-L9-A443       TCGA-L9-A444 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-MP-A4T8       TCGA-MP-A4TA       TCGA-MP-A4TC 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-MP-A4TD       TCGA-05-4244       TCGA-05-4249       TCGA-05-4250 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-05-4389       TCGA-05-4390       TCGA-05-4395       TCGA-05-4397 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-05-4398       TCGA-05-4403       TCGA-05-4415       TCGA-05-4417 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-05-4420       TCGA-05-4422       TCGA-05-4424       TCGA-05-4425 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-05-4426       TCGA-05-4430       TCGA-05-4432       TCGA-05-4433 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-05-5423       TCGA-05-5425       TCGA-05-5428       TCGA-05-5429 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-05-5715       TCGA-35-4122       TCGA-35-4123       TCGA-35-5375 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-38-4625       TCGA-38-4626       TCGA-38-4627       TCGA-38-4628 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-38-4632       TCGA-38-A44F       TCGA-44-2657       TCGA-44-2665 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-44-3396       TCGA-44-3398       TCGA-44-3918       TCGA-44-3919 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-44-4112       TCGA-44-6144       TCGA-44-6148       TCGA-44-6775 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-44-A479       TCGA-44-A47A       TCGA-44-A47B       TCGA-44-A47G 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-44-A4SU       TCGA-49-4486       TCGA-49-4487       TCGA-49-4488 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-49-4494       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-49-6744 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-49-6767       TCGA-50-5051       TCGA-50-5055       TCGA-50-5066 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-50-5931       TCGA-50-5942       TCGA-50-5944       TCGA-50-6593 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-50-6673       TCGA-50-8460       TCGA-53-7624       TCGA-53-A4EZ 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-5899       TCGA-55-6642       TCGA-55-6712       TCGA-55-6970 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-6971       TCGA-55-6972       TCGA-55-6980       TCGA-55-6981 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-6983       TCGA-55-6985       TCGA-55-7227       TCGA-55-7281 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-7570       TCGA-55-7574       TCGA-55-7576       TCGA-55-7727 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-7728       TCGA-55-7815       TCGA-55-7903       TCGA-55-7907 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-7910       TCGA-55-7911       TCGA-55-7913       TCGA-55-7994 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-7995       TCGA-55-8085       TCGA-55-8087       TCGA-55-8089 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-8092       TCGA-55-8094       TCGA-55-8097       TCGA-55-8206 
"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-55-8512       TCGA-55-8513       TCGA-55-8514 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-8614       TCGA-55-8615       TCGA-55-8616       TCGA-55-8620 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-A48Y       TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A493 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-55-A494       TCGA-55-A4DG       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-64-1676       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-71-6725       TCGA-71-8520       TCGA-73-4659       TCGA-73-4666 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-73-4668       TCGA-73-4670       TCGA-73-4675       TCGA-73-4676 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-73-4677       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-78-7167       TCGA-78-7220       TCGA-78-7535       TCGA-78-7536 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-78-7537       TCGA-78-7539       TCGA-78-7540       TCGA-78-7542 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-78-8640       TCGA-78-8648       TCGA-78-8655       TCGA-78-8662 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-80-5608       TCGA-83-5908       TCGA-86-6562       TCGA-86-7701 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-7711       TCGA-86-7713       TCGA-86-7714       TCGA-86-7953 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-7954       TCGA-86-7955       TCGA-86-8054       TCGA-86-8055 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-8056       TCGA-86-8073       TCGA-86-8074       TCGA-86-8075 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-8076       TCGA-86-8278       TCGA-86-8279       TCGA-86-8280 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-8358       TCGA-86-8359       TCGA-86-8585       TCGA-86-8668 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-8669       TCGA-86-8671       TCGA-86-8672       TCGA-86-8673 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-86-8674       TCGA-86-A456       TCGA-86-A4JF       TCGA-86-A4P7 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-91-6828       TCGA-91-6829       TCGA-91-6835       TCGA-91-6840 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-91-A4BD       TCGA-93-7347       TCGA-93-7348       TCGA-93-A4JN 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-93-A4JO       TCGA-93-A4JP       TCGA-95-7944       TCGA-95-8039 
"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-99-7458       TCGA-99-8025       TCGA-99-8028 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-99-8032       TCGA-99-8033       TCGA-J2-A4AD       TCGA-J2-A4AE 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-J2-A4AG       TCGA-L4-A4E5       TCGA-L4-A4E6       TCGA-MN-A4N4 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-MN-A4N5       TCGA-MP-A4SV       TCGA-MP-A4SW       TCGA-MP-A4SY 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-MP-A4T2       TCGA-MP-A4T6       TCGA-MP-A4T7       TCGA-MP-A4T9 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-MP-A4TE       TCGA-MP-A4TF       TCGA-MP-A4TH       TCGA-MP-A4TI 
"TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" "TMEM49 WILD-TYPE" 
      TCGA-MP-A4TK       TCGA-MP-A5C7       TCGA-NJ-A4YQ 
"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                        30   373
D56V14, multiclass
                                  clus
vv                                 TMEM49 MUTATED TMEM49 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     0               30
  WHITE                                         5              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"
D56V15, binary
                  cls
clus                 0   1
  TMEM49 MUTATED     0   4
  TMEM49 WILD-TYPE   6 347
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM49 MUTATED      0    4
  TMEM49 WILD-TYPE    6  347
                        clus
vv                       TMEM49 MUTATED TMEM49 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              4              347
[1] 2 2
[1] FALSE

Clustering(57) Variable = HSPA8 MUTATION ANALYSIS
D57V1, survival
                 sevent
clus2               0   1
  HSPA8 MUTATED     5   4
  HSPA8 WILD-TYPE 293 167
  HSPA8 MUTATED HSPA8 WILD-TYPE 
              9             460 
  HSPA8 MUTATED HSPA8 WILD-TYPE 
              4             167 
$`HSPA8 MUTATED`
TCGA-55-1592 TCGA-50-5946 TCGA-53-7624 TCGA-69-7978 TCGA-73-4666 TCGA-78-7147 
       23.05        53.16        34.29         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-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       29.98        12.00        30.02        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       25.02        24.00         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       37.71        49.05        44.61         4.37        46.98        44.42 
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-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       19.46         7.17        36.07        18.87        23.64        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
        8.55        15.98        15.32         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
       53.29        55.33        22.26        20.52        71.47       101.72 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        47.41        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       14.27        78.67         8.45        15.12        48.46        60.72 
TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       57.53        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       30.54        13.94        35.21        30.58        14.30        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        5.62        42.51        40.73        15.25        46.03        53.65 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26        31.30        28.67        20.02 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       27.09        32.71        22.03         3.91        23.15        25.41 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 
       15.39        18.64        11.28        34.19        17.65        18.44 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 
       19.82        29.23        29.72        15.19        23.08         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       17.79        23.64        15.65        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       17.56        15.72        14.47         0.36        13.74        20.28 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
        1.58        12.33        20.71        21.40         3.25         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       56.81        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-69-7760 TCGA-69-7761 TCGA-69-7763 
       14.73         5.72         4.64         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        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        19.43         8.42         6.90 
TCGA-73-4659 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       23.38        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
       50.33        66.64        77.85        43.82        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       36.66       108.66       100.57       163.10        27.16         5.69 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      104.19       238.29        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       53.33        26.01        39.35       232.18        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
      110.50        93.11        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 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-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
       37.74         4.08        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        11.61        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        12.23        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
       23.61         1.08        19.00        41.82        18.67        12.39 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       27.29         2.76        19.89        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       61.48        25.48        18.54         0.59        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       20.58        21.44        19.76        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE 
       34.85        36.76         1.45        21.57        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       32.48        19.00        14.30        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       41.59        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.49         0.43        19.82        59.11 

  HSPA8 MUTATED HSPA8 WILD-TYPE 
           4.41            0.00 
  HSPA8 MUTATED HSPA8 WILD-TYPE 
          53.16          238.29 
  HSPA8 MUTATED HSPA8 WILD-TYPE 
         21.470          21.455 
[1] "4.4 - 53.2 (21.5)"  "0.0 - 238.3 (21.5)"
[1] "hr=" "1.6"
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      119      130        46        64         69
                 vv
clus              STAGE IIIB STAGE IV
  HSPA8 MUTATED            0        2
  HSPA8 WILD-TYPE         11       22
D57V3, multiclass
            clus
vv           HSPA8 MUTATED HSPA8 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             119
  STAGE IB               2             130
  STAGE IIA              0              46
  STAGE IIB              2              64
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               2              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
  HSPA8 MUTATED     2   6   0   1
  HSPA8 WILD-TYPE 154 255  43  17
D57V4, multiclass
    clus
vv   HSPA8 MUTATED HSPA8 WILD-TYPE
  T1             2             154
  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 301  87    72
D57V5, multiclass
       clus
vv      HSPA8 MUTATED HSPA8 WILD-TYPE
  N0                7             301
  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 256 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPA8 MUTATED      4    5
  HSPA8 WILD-TYPE  256  216
        clus
vv       HSPA8 MUTATED HSPA8 WILD-TYPE
  FEMALE             4             256
  MALE               5             216
[1] 2 2
[1] FALSE
D57V8, binary
                 cls
clus                0   1
  HSPA8 MUTATED     6   1
  HSPA8 WILD-TYPE 378  54
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPA8 MUTATED      6    1
  HSPA8 WILD-TYPE  378   54
     clus
vv    HSPA8 MUTATED HSPA8 WILD-TYPE
  NO              6             378
  YES             1              54
[1] 2 2
[1] FALSE
D57V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  HSPA8 MUTATED                            0                                 3
  HSPA8 WILD-TYPE                         17                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  HSPA8 MUTATED                                                    6
  HSPA8 WILD-TYPE                                                290
                 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                                      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                    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 305  12   4  25
D57V13, multiclass
    clus
vv   HSPA8 MUTATED HSPA8 WILD-TYPE
  R0             7             305
  R1             0              12
  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                        30   369
D57V14, multiclass
                                  clus
vv                                 HSPA8 MUTATED HSPA8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              30
  WHITE                                        9             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"
D57V15, binary
                 cls
clus                0   1
  HSPA8 MUTATED     1   5
  HSPA8 WILD-TYPE   5 346
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HSPA8 MUTATED      1    5
  HSPA8 WILD-TYPE    5  346
                        clus
vv                       HSPA8 MUTATED HSPA8 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             5             346
[1] 2 2
[1] FALSE

Clustering(58) Variable = CD244 MUTATION ANALYSIS
D58V1, survival
                 sevent
clus2               0   1
  CD244 MUTATED     8   4
  CD244 WILD-TYPE 290 167
  CD244 MUTATED CD244 WILD-TYPE 
             12             457 
  CD244 MUTATED CD244 WILD-TYPE 
              4             167 
$`CD244 MUTATED`
TCGA-44-7670 TCGA-44-2656 TCGA-44-7672 TCGA-50-5045 TCGA-55-8092 TCGA-55-8096 
       29.00        46.98        23.64        71.47         5.06        23.64 
TCGA-55-8506 TCGA-69-7979 TCGA-75-5147 TCGA-78-7220 TCGA-86-8358 TCGA-97-A4M5 
        0.36        13.41        43.82        26.53        21.47        20.84 

$`CD244 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       18.31        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       29.98        12.00        30.02        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       25.02        24.00         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2665 
       37.71        49.05        44.61         4.37        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-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
        7.17        36.07        18.87        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       22.26        20.52       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       49.28         8.22         9.27        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
        3.91        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99        36.79        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       13.94        35.21        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
      107.21        70.26        31.30        28.67        20.02        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
       32.71        22.03         3.91        23.15        25.41        15.39 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       18.64        11.28        34.19        17.65        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8094 TCGA-55-8097 
       29.23        29.72        15.19        23.08        17.79        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       29.19        22.16        15.42        17.56        15.72        14.47 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       13.74        20.28        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.62        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        3.25         0.92        15.81        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 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-69-7760 
       18.84        14.04        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 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-69-A59K 
        4.41        13.51        14.01        13.45         4.24        19.43 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        8.42         6.90        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       30.31         9.24         1.25        50.33        66.64        77.85 
TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       85.15        49.84        36.66       108.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 
       64.90        22.92         9.57       104.19       238.29        88.14 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 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        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.18        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
       19.00        41.82        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       15.39        16.41        14.30        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       19.76        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.57        18.08        35.47        32.48        19.00        14.30 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        47.08         0.49         0.43        19.82 
TCGA-O1-A52J 
       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 
          23.64           21.44 
[1] "0.4 - 71.5 (23.6)"  "0.0 - 238.3 (21.4)"
[1] "hr=" "1.1"
D58V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  CD244 MUTATED         0        2        5         1         2          1
  CD244 WILD-TYPE       4      119      127        45        64         69
                 vv
clus              STAGE IIIB STAGE IV
  CD244 MUTATED            0        0
  CD244 WILD-TYPE         11       24
D58V3, multiclass
            clus
vv           CD244 MUTATED CD244 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             119
  STAGE IB               5             127
  STAGE IIA              1              45
  STAGE IIB              2              64
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              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
  CD244 MUTATED     3   7   2   0
  CD244 WILD-TYPE 153 254  41  18
D58V4, multiclass
    clus
vv   CD244 MUTATED CD244 WILD-TYPE
  T1             3             153
  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 299  87    71
D58V5, multiclass
       clus
vv      CD244 MUTATED CD244 WILD-TYPE
  N0                9             299
  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 252 217
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      8    4
  CD244 WILD-TYPE  252  217
        clus
vv       CD244 MUTATED CD244 WILD-TYPE
  FEMALE             8             252
  MALE               4             217
[1] 2 2
[1] FALSE
D58V8, binary
                 cls
clus                0   1
  CD244 MUTATED     9   2
  CD244 WILD-TYPE 375  53
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      9    2
  CD244 WILD-TYPE  375   53
     clus
vv    CD244 MUTATED CD244 WILD-TYPE
  NO              9             375
  YES             2              53
[1] 2 2
[1] FALSE
D58V9, continuous
[1] "Remove cluster labels:" "CD244 MUTATED"         
clus
  CD244 MUTATED CD244 WILD-TYPE 
              2             120 
     TCGA-44-6147      TCGA-44-A47F      TCGA-49-6742      TCGA-55-7573 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7914      TCGA-55-8205      TCGA-55-8511 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8621      TCGA-55-A491      TCGA-55-A492 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-64-1677      TCGA-73-4662      TCGA-73-7498      TCGA-93-8067 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-35-4122      TCGA-35-4123      TCGA-35-5375 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-44-3396      TCGA-44-3918      TCGA-44-4112      TCGA-44-6144 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-7660      TCGA-49-4486      TCGA-49-4494 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-49-4505      TCGA-49-4506      TCGA-49-4510      TCGA-49-6743 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-49-6744      TCGA-53-7624      TCGA-53-A4EZ      TCGA-55-5899 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7574      TCGA-55-7910      TCGA-55-7913 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-55-7995      TCGA-55-8089      TCGA-55-8208      TCGA-55-8507 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-55-8508      TCGA-55-8512      TCGA-55-8513      TCGA-55-8620 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A494      TCGA-62-8394 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-62-8395      TCGA-62-8397      TCGA-62-8398      TCGA-62-8399 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-62-8402      TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-62-A46S      TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-62-A470      TCGA-62-A471      TCGA-62-A472      TCGA-64-1681 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-64-5775      TCGA-64-5778      TCGA-69-7974      TCGA-69-8254 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-71-6725      TCGA-71-8520      TCGA-73-4659      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-73-7499      TCGA-75-5122      TCGA-83-5908      TCGA-86-6562 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-86-6851      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7953      TCGA-86-7954      TCGA-86-7955 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-86-8054      TCGA-86-8055      TCGA-86-8056      TCGA-86-8073 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8075      TCGA-86-8076      TCGA-86-8278 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8280      TCGA-86-8281      TCGA-86-8359 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-A456 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6829      TCGA-91-6849 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-93-7347      TCGA-93-7348      TCGA-93-A4JN      TCGA-93-A4JO 
"CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" "CD244 WILD-TYPE" 
     TCGA-95-7567      TCGA-99-7458      TCGA-MN-A4N4      TCGA-MN-A4N5 
"CD244 WILD-TYPE" "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                         16                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CD244 MUTATED                                                    9
  CD244 WILD-TYPE                                                287
                 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                                      16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  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"
D58V11, continuous
D58V12, continuous
                 vv
clus               R0  R1  R2  RX
  CD244 MUTATED     5   0   0   0
  CD244 WILD-TYPE 307  12   4  25
D58V13, multiclass
    clus
vv   CD244 MUTATED CD244 WILD-TYPE
  R0             5             307
  R1             0              12
  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                        29   368
D58V14, multiclass
                                  clus
vv                                 CD244 MUTATED CD244 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              29
  WHITE                                       10             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"
D58V15, binary
                 cls
clus                0   1
  CD244 MUTATED     1   9
  CD244 WILD-TYPE   5 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      1    9
  CD244 WILD-TYPE    5  342
                        clus
vv                       CD244 MUTATED CD244 WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             9             342
[1] 2 2
[1] FALSE

Clustering(59) Variable = KIF18B MUTATION ANALYSIS
D59V1, survival
                  sevent
clus2                0   1
  KIF18B MUTATED     3   1
  KIF18B WILD-TYPE 295 170
  KIF18B MUTATED KIF18B WILD-TYPE 
               4              465 
  KIF18B MUTATED KIF18B WILD-TYPE 
               1              170 
$`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-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       17.29        16.54         2.86        15.68        15.65        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       18.18        17.92        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 
       24.30        23.80         6.35        10.09        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 
       31.23         2.43        10.09        50.07        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       29.98        12.00        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         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-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       55.33        22.26        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       53.16        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 
       34.29        30.54        13.94        35.21        30.58        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       80.52         5.62        42.51        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       53.65         3.88        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26        31.30        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       20.02        27.09        32.71        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       25.41        15.39        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.44        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42        17.56        15.72        14.47         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       14.66         1.58        12.33        20.71        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       29.92        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-67-4679 
       28.41        51.25        28.47        18.84        14.04        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        19.43         8.42         6.90 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       23.38        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
        1.25        50.33        66.64        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       49.84        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
       22.92         9.57       104.19       238.29        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
        1.08        19.00        41.82        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       25.48        18.54         0.59        15.91        18.67         5.39 
TCGA-97-8175 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-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       36.76         1.45        21.57        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       19.00        14.30        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       49.35        37.35        86.04        58.85         5.49        41.59 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        24.36        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        74.33         0.13         1.64        47.08         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-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           21.470 
[1] "4.0 - 56.8 (25.0)"  "0.0 - 238.3 (21.5)"
[1] "hr=" "1.5"
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      119      132        46        65         69
                  vv
clus               STAGE IIIB STAGE IV
  KIF18B MUTATED            0        0
  KIF18B WILD-TYPE         11       24
D59V3, multiclass
            clus
vv           KIF18B MUTATED KIF18B WILD-TYPE
  STAGE I                 0                4
  STAGE IA                2              119
  STAGE IB                0              132
  STAGE IIA               0               46
  STAGE IIB               1               65
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               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
  KIF18B MUTATED     2   0   2   0
  KIF18B WILD-TYPE 154 261  41  18
D59V4, multiclass
    clus
vv   KIF18B MUTATED KIF18B WILD-TYPE
  T1              2              154
  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 305  88    72
D59V5, multiclass
       clus
vv      KIF18B MUTATED KIF18B WILD-TYPE
  N0                 3              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"
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 258 219
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF18B MUTATED      2    2
  KIF18B WILD-TYPE  258  219
        clus
vv       KIF18B MUTATED KIF18B WILD-TYPE
  FEMALE              2              258
  MALE                2              219
[1] 2 2
[1] FALSE
D59V8, binary
                  cls
clus                 0   1
  KIF18B MUTATED     1   1
  KIF18B WILD-TYPE 383  54
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF18B MUTATED      1    1
  KIF18B WILD-TYPE  383   54
     clus
vv    KIF18B MUTATED KIF18B WILD-TYPE
  NO               1              383
  YES              1               54
[1] 2 2
[1] FALSE
D59V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KIF18B MUTATED                            0                                 1
  KIF18B WILD-TYPE                         17                               101
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KIF18B MUTATED                                                    3
  KIF18B WILD-TYPE                                                293
                  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                                       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"
D59V11, continuous
D59V12, continuous
[1] "Remove cluster labels:" "KIF18B MUTATED"        
clus
  KIF18B MUTATED KIF18B WILD-TYPE 
               1              257 
      TCGA-05-4384       TCGA-05-4396       TCGA-05-4405       TCGA-05-4410 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-05-4427       TCGA-05-5420       TCGA-38-7271       TCGA-44-6147 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-6776       TCGA-44-7661       TCGA-44-7670       TCGA-44-8119 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-A47F       TCGA-55-1592       TCGA-55-1595       TCGA-55-7724 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7725       TCGA-55-7726       TCGA-55-7914       TCGA-55-8205 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8511       TCGA-55-8621       TCGA-55-A48X       TCGA-55-A491 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-A492       TCGA-64-1677       TCGA-73-4662       TCGA-73-7498 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7166       TCGA-78-7633       TCGA-78-8660       TCGA-80-5607 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-91-6836       TCGA-91-A4BC       TCGA-93-8067       TCGA-93-A4JQ 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-95-7043       TCGA-95-7562       TCGA-95-7947       TCGA-95-7948 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-95-A4VK       TCGA-95-A4VN       TCGA-97-8172       TCGA-97-A4LX 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-A4M2       TCGA-97-A4M3       TCGA-97-A4M7       TCGA-J2-8194 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-L9-A443       TCGA-L9-A444       TCGA-MN-A4N1       TCGA-MP-A4T8 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A4TA       TCGA-MP-A4TC       TCGA-05-4390       TCGA-05-4415 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-05-4417       TCGA-05-4433       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-A44F       TCGA-44-2656 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-2657       TCGA-44-3396       TCGA-44-3398       TCGA-44-3918 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-4112       TCGA-44-5644       TCGA-44-5645       TCGA-44-6144 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-6145       TCGA-44-6148       TCGA-44-6774       TCGA-44-6775 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-6777       TCGA-44-6778       TCGA-44-6779       TCGA-44-7659 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-7660       TCGA-44-7662       TCGA-44-7667       TCGA-44-7669 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-7672       TCGA-44-8117       TCGA-44-8120       TCGA-44-A479 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-A47A       TCGA-44-A47B       TCGA-44-A47G       TCGA-44-A4SS 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-A4SU       TCGA-49-4486       TCGA-49-4494       TCGA-49-4505 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-53-7624       TCGA-53-7626       TCGA-53-7813       TCGA-53-A4EZ 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-5899       TCGA-55-6642       TCGA-55-6712       TCGA-55-6971 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7227       TCGA-55-7283       TCGA-55-7570       TCGA-55-7574 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7576       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-55-7913       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-55-8299 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8301       TCGA-55-8302       TCGA-55-8506       TCGA-55-8507 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8512       TCGA-55-8514       TCGA-55-8615       TCGA-55-8620 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-A48Y       TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A493 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-A494       TCGA-62-8398       TCGA-64-1681       TCGA-64-5774 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-64-5775       TCGA-64-5778       TCGA-64-5779       TCGA-64-5781 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-69-7761       TCGA-69-7763       TCGA-69-7764       TCGA-69-7765 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-69-7974       TCGA-69-7979       TCGA-69-8253       TCGA-69-8255 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-69-A59K       TCGA-73-4659       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-75-6214 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-75-7025       TCGA-75-7027       TCGA-75-7031       TCGA-78-7145 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7146       TCGA-78-7147       TCGA-78-7148       TCGA-78-7149 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7150       TCGA-78-7152       TCGA-78-7153       TCGA-78-7154 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7155       TCGA-78-7156       TCGA-78-7158       TCGA-78-7159 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7160       TCGA-78-7161       TCGA-78-7162       TCGA-78-7163 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7167       TCGA-78-7220       TCGA-78-7535       TCGA-78-7536 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7537       TCGA-78-7539       TCGA-78-7542       TCGA-78-8640 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-8648       TCGA-78-8655       TCGA-78-8662       TCGA-80-5608 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-83-5908       TCGA-86-6851       TCGA-86-7711       TCGA-86-7714 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-7954       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-86-8281       TCGA-86-8358 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8359       TCGA-86-8669       TCGA-86-8673       TCGA-86-8674 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-A456       TCGA-91-6829       TCGA-91-6830       TCGA-91-6840 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-91-6849       TCGA-91-8499       TCGA-93-7347       TCGA-93-7348 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-93-A4JN       TCGA-93-A4JO       TCGA-95-7567       TCGA-95-7944 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-95-A4VP       TCGA-97-7546       TCGA-97-7553       TCGA-97-7554 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-7941       TCGA-97-8171       TCGA-97-8174       TCGA-97-8176 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-8179       TCGA-97-A4M0       TCGA-97-A4M1       TCGA-97-A4M5 
"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-A4AD       TCGA-J2-A4AG       TCGA-L4-A4E5       TCGA-L4-A4E6 
"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-A4T9 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A4TE       TCGA-MP-A4TF       TCGA-MP-A4TH       TCGA-MP-A4TI 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A4TK       TCGA-MP-A5C7       TCGA-NJ-A4YG       TCGA-NJ-A4YI 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-O1-A52J 
"KIF18B WILD-TYPE" 
                  vv
clus                R0  R1  R2  RX
  KIF18B MUTATED     2   1   1   0
  KIF18B WILD-TYPE 310  11   3  25
D59V13, multiclass
    clus
vv   KIF18B MUTATED KIF18B WILD-TYPE
  R0              2              310
  R1              1               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
  KIF18B MUTATED                                  0     0
  KIF18B WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KIF18B MUTATED                           1     1
  KIF18B WILD-TYPE                        29   377
D59V14, multiclass
[1] "Remove cluster labels:" "KIF18B MUTATED"        
clus
  KIF18B MUTATED KIF18B WILD-TYPE 
               2              414 
      TCGA-38-4629       TCGA-38-4630       TCGA-38-4631       TCGA-38-6178 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-38-7271       TCGA-44-2661       TCGA-44-6146       TCGA-44-6147 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-6776       TCGA-44-7661       TCGA-44-7670       TCGA-44-7671 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-8119       TCGA-44-A47F       TCGA-49-4501       TCGA-49-6742 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-49-6745       TCGA-49-6761       TCGA-50-5932       TCGA-50-5935 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-6597       TCGA-55-1592       TCGA-55-1595       TCGA-55-6978 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-6979       TCGA-55-7284       TCGA-55-7573       TCGA-55-7724 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7725       TCGA-55-7726       TCGA-55-7914       TCGA-55-8090 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8091       TCGA-55-8203       TCGA-55-8204       TCGA-55-8205 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8207       TCGA-55-8511       TCGA-55-8619       TCGA-55-8621 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-A48X       TCGA-55-A491       TCGA-55-A492       TCGA-55-A4DF 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-64-1677       TCGA-67-6217       TCGA-73-4658       TCGA-73-4662 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-73-7498       TCGA-78-7166       TCGA-78-7633       TCGA-91-6836 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-91-7771       TCGA-91-A4BC       TCGA-93-8067       TCGA-93-A4JQ 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-95-7043       TCGA-95-7562       TCGA-95-7947       TCGA-95-7948 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-95-A4VK       TCGA-95-A4VN       TCGA-97-8172       TCGA-97-A4LX 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-A4M2       TCGA-97-A4M3       TCGA-97-A4M7       TCGA-J2-8192 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-J2-8194       TCGA-L9-A443       TCGA-L9-A444       TCGA-MN-A4N1 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A4TA       TCGA-MP-A4TC       TCGA-MP-A4TD       TCGA-35-4122 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-35-4123       TCGA-35-5375       TCGA-38-4625       TCGA-38-4626 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-38-4627       TCGA-38-4628       TCGA-38-4632       TCGA-38-A44F 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-2656       TCGA-44-2657       TCGA-44-2665       TCGA-44-3396 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-3398       TCGA-44-3918       TCGA-44-3919       TCGA-44-4112 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-5643       TCGA-44-5644       TCGA-44-5645       TCGA-44-6144 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-6145       TCGA-44-6148       TCGA-44-6774       TCGA-44-6775 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-6777       TCGA-44-6778       TCGA-44-6779       TCGA-44-7659 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-7660       TCGA-44-7662       TCGA-44-7667       TCGA-44-7669 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-7672       TCGA-44-8117       TCGA-44-8120       TCGA-44-A479 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-A47A       TCGA-44-A47B       TCGA-44-A47G       TCGA-44-A4SS 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-44-A4SU       TCGA-49-4486       TCGA-49-4487       TCGA-49-4488 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-49-4490       TCGA-49-4494       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-49-6743       TCGA-49-6744       TCGA-49-6767       TCGA-50-5044 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-5045       TCGA-50-5049       TCGA-50-5051       TCGA-50-5055 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-5066       TCGA-50-5068       TCGA-50-5072       TCGA-50-5930 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-5931       TCGA-50-5933       TCGA-50-5936       TCGA-50-5939 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-5941       TCGA-50-5942       TCGA-50-5944       TCGA-50-5946 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-6590       TCGA-50-6591       TCGA-50-6592       TCGA-50-6593 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-6594       TCGA-50-6595       TCGA-50-6673       TCGA-50-7109 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-50-8457       TCGA-50-8459       TCGA-50-8460       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-55-5899 
"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-55-6980       TCGA-55-6981       TCGA-55-6982 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-6983       TCGA-55-6984       TCGA-55-6985       TCGA-55-6986 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-6987       TCGA-55-7227       TCGA-55-7281       TCGA-55-7283 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7570       TCGA-55-7574       TCGA-55-7576       TCGA-55-7727 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7728       TCGA-55-7816       TCGA-55-7903       TCGA-55-7907 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7910       TCGA-55-7911       TCGA-55-7913       TCGA-55-7994 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-7995       TCGA-55-8085       TCGA-55-8087       TCGA-55-8089 
"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-55-8206       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-55-8512       TCGA-55-8513 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8514       TCGA-55-8614       TCGA-55-8615       TCGA-55-8616 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-8620       TCGA-55-A48Y       TCGA-55-A48Z       TCGA-55-A490 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-55-A493       TCGA-55-A494       TCGA-55-A4DG       TCGA-62-8394 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-62-8395       TCGA-62-8397       TCGA-62-8398       TCGA-62-8399 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-62-8402       TCGA-62-A46O       TCGA-62-A46P       TCGA-62-A46R 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-62-A46S       TCGA-62-A46U       TCGA-62-A46V       TCGA-62-A46Y 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-62-A470       TCGA-62-A471       TCGA-62-A472       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-69-7760       TCGA-69-7761       TCGA-69-7763       TCGA-69-7764 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-69-7765       TCGA-69-7973       TCGA-69-7974       TCGA-69-7978 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-69-7979       TCGA-69-7980       TCGA-69-8253       TCGA-69-8254 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-69-8255       TCGA-69-A59K       TCGA-71-6725       TCGA-71-8520 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-73-4659       TCGA-73-4666       TCGA-73-4668       TCGA-73-4670 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-73-4675       TCGA-73-4676       TCGA-73-4677       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-78-7167       TCGA-78-7220 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7535       TCGA-78-7536       TCGA-78-7539       TCGA-78-7540 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-78-7542       TCGA-83-5908       TCGA-86-6562       TCGA-86-6851 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-7701       TCGA-86-7711       TCGA-86-7713       TCGA-86-7714 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-7953       TCGA-86-7954       TCGA-86-7955       TCGA-86-8054 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8055       TCGA-86-8056       TCGA-86-8073       TCGA-86-8074 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8075       TCGA-86-8076       TCGA-86-8278       TCGA-86-8279 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8280       TCGA-86-8281       TCGA-86-8358       TCGA-86-8359 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8585       TCGA-86-8668       TCGA-86-8669       TCGA-86-8671 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-8672       TCGA-86-8673       TCGA-86-8674       TCGA-86-A456 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-86-A4JF       TCGA-86-A4P7       TCGA-86-A4P8       TCGA-91-6828 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-91-6829       TCGA-91-6830       TCGA-91-6831       TCGA-91-6835 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-91-6840       TCGA-91-6847       TCGA-91-6848       TCGA-91-6849 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-91-8496       TCGA-91-8497       TCGA-91-8499       TCGA-91-A4BD 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-93-7347       TCGA-93-7348       TCGA-93-A4JN       TCGA-93-A4JO 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-93-A4JP       TCGA-95-7039       TCGA-95-7567       TCGA-95-7944 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-95-8039       TCGA-95-8494       TCGA-95-A4VP       TCGA-97-7546 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-7547       TCGA-97-7552       TCGA-97-7553       TCGA-97-7554 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-7937       TCGA-97-7938       TCGA-97-7941       TCGA-97-8171 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-8174       TCGA-97-8175       TCGA-97-8176       TCGA-97-8177 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-8179       TCGA-97-8552       TCGA-97-A4M0       TCGA-97-A4M1 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-97-A4M5       TCGA-97-A4M6       TCGA-99-7458       TCGA-99-8025 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-99-8028       TCGA-99-8032       TCGA-99-8033       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-MN-A4N4       TCGA-MN-A4N5       TCGA-MP-A4SW       TCGA-MP-A4SY 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A4T2       TCGA-MP-A4T4       TCGA-MP-A4T6       TCGA-MP-A4T9 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A4TE       TCGA-MP-A4TF       TCGA-MP-A4TH       TCGA-MP-A4TI 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-MP-A5C7       TCGA-NJ-A4YF       TCGA-NJ-A4YG       TCGA-NJ-A4YI 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-NJ-A4YP       TCGA-NJ-A4YQ       TCGA-NJ-A55A       TCGA-NJ-A55O 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
      TCGA-NJ-A55R       TCGA-O1-A52J 
"KIF18B WILD-TYPE" "KIF18B WILD-TYPE" 
D59V15, binary
                  cls
clus                 0   1
  KIF18B MUTATED     0   2
  KIF18B WILD-TYPE   6 349
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF18B MUTATED      0    2
  KIF18B WILD-TYPE    6  349
                        clus
vv                       KIF18B MUTATED KIF18B WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              2              349
[1] 2 2
[1] FALSE

Clustering(60) Variable = PDE6A MUTATION ANALYSIS
D60V1, survival
                 sevent
clus2               0   1
  PDE6A MUTATED    10   6
  PDE6A WILD-TYPE 288 165
  PDE6A MUTATED PDE6A WILD-TYPE 
             16             453 
  PDE6A MUTATED PDE6A WILD-TYPE 
              6             165 
$`PDE6A MUTATED`
TCGA-05-4382 TCGA-MN-A4N1 TCGA-MP-A4TA TCGA-44-5644 TCGA-53-7624 TCGA-55-6642 
       19.96        27.19        31.23        28.37        34.29        80.52 
TCGA-55-6972 TCGA-55-8299 TCGA-55-8507 TCGA-55-A4DG TCGA-62-A46O TCGA-67-3771 
       53.65        15.42        13.74        19.99        47.80        20.05 
TCGA-73-4659 TCGA-73-4668 TCGA-91-6828 TCGA-NJ-A4YQ 
       23.38        15.35        10.62        47.08 

$`PDE6A WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       14.01         9.96         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD 
       23.80         6.35        10.09         5.29         2.43        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       47.05        19.00         2.99        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-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-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 
       44.61         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-44-5645 
       38.24        34.06        33.73        26.56        33.30        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       23.77        19.56        23.15        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
       61.28        16.44        22.72        19.46         7.17        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       18.87        23.64        12.66         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
        9.44        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 
       29.46        29.75        55.89        53.29        55.33        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       49.28         8.22         9.27        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
        3.91        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
       10.13        36.99        36.79        27.25        30.54        13.94 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       35.21        30.58        14.30         5.62        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       15.25        46.03         3.88        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       92.81        24.99        40.54       107.21        70.26        31.30 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
       28.67        20.02        27.09        32.71        22.03         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
       23.15        25.41        15.39        18.64        11.28        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       23.08         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
       22.16        17.56        15.72        14.47         0.36        20.28 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
        1.58        12.33        20.71        21.40         3.25         0.92 
TCGA-55-A494 TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       15.81         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-64-1679 
       13.61        39.25        40.96        29.92        56.81        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3772 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-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        13.41        13.51        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4666 TCGA-73-4670 
        4.24        19.43         8.42         6.90        26.30         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       30.31         9.24         1.25        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 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        11.61 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-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-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        12.23        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
       23.61         1.08        19.00        41.82        18.67        12.39 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       27.29         2.76        19.89        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       61.48        25.48        18.54         0.59        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       20.58        21.44        19.76        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE 
       34.85        36.76         1.45        21.57        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       32.48        19.00        14.30        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       41.59        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A 
       73.91        71.05        74.33         0.13         1.64         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  PDE6A MUTATED PDE6A WILD-TYPE 
          10.62            0.00 
  PDE6A MUTATED PDE6A WILD-TYPE 
          80.52          238.29 
  PDE6A MUTATED PDE6A WILD-TYPE 
         25.285          21.440 
[1] "10.6 - 80.5 (25.3)" "0.0 - 238.3 (21.4)"
[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      114      127        45        65         69
                 vv
clus              STAGE IIIB STAGE IV
  PDE6A MUTATED            0        1
  PDE6A WILD-TYPE         11       23
D60V3, multiclass
            clus
vv           PDE6A MUTATED PDE6A WILD-TYPE
  STAGE I                0               4
  STAGE IA               7             114
  STAGE IB               5             127
  STAGE IIA              1              45
  STAGE IIB              1              65
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               1              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
  PDE6A MUTATED     7   9   0   0
  PDE6A WILD-TYPE 149 252  43  18
D60V4, multiclass
    clus
vv   PDE6A MUTATED PDE6A WILD-TYPE
  T1             7             149
  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 295  87    71
D60V5, multiclass
       clus
vv      PDE6A MUTATED PDE6A WILD-TYPE
  N0               13             295
  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 252 213
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE6A MUTATED      8    8
  PDE6A WILD-TYPE  252  213
        clus
vv       PDE6A MUTATED PDE6A WILD-TYPE
  FEMALE             8             252
  MALE               8             213
[1] 2 2
[1] FALSE
D60V8, binary
                 cls
clus                0   1
  PDE6A MUTATED    14   1
  PDE6A WILD-TYPE 370  54
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE6A MUTATED     14    1
  PDE6A WILD-TYPE  370   54
     clus
vv    PDE6A MUTATED PDE6A WILD-TYPE
  NO             14             370
  YES             1              54
[1] 2 2
[1] FALSE
D60V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  PDE6A MUTATED                            0                                 1
  PDE6A WILD-TYPE                         17                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PDE6A MUTATED                                                   13
  PDE6A WILD-TYPE                                                283
                 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                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  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                               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 298  12   4  24
D60V13, multiclass
    clus
vv   PDE6A MUTATED PDE6A WILD-TYPE
  R0            14             298
  R1             0              12
  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                        28   366
D60V14, multiclass
                                  clus
vv                                 PDE6A MUTATED PDE6A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    2              28
  WHITE                                       12             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"
D60V15, binary
                 cls
clus                0   1
  PDE6A MUTATED     1  13
  PDE6A WILD-TYPE   5 338
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDE6A MUTATED      1   13
  PDE6A WILD-TYPE    5  338
                        clus
vv                       PDE6A MUTATED PDE6A WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            13             338
[1] 2 2
[1] FALSE

Clustering(61) Variable = CHRND MUTATION ANALYSIS
D61V1, survival
                 sevent
clus2               0   1
  CHRND MUTATED    12   3
  CHRND WILD-TYPE 286 168
  CHRND MUTATED CHRND WILD-TYPE 
             15             454 
  CHRND MUTATED CHRND WILD-TYPE 
              3             168 
$`CHRND MUTATED`
TCGA-05-4418 TCGA-55-A492 TCGA-95-7947 TCGA-05-4420 TCGA-05-4432 TCGA-38-4632 
        9.01        19.59        15.68        29.98        25.02        44.61 
TCGA-44-3918 TCGA-44-5644 TCGA-44-7662 TCGA-50-5049 TCGA-50-8459 TCGA-55-7907 
       34.06        28.37         7.17       101.72        36.79        11.28 
TCGA-62-8399 TCGA-64-5778 TCGA-86-8358 
       88.64        42.90        21.47 

$`CHRND WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4427 
       19.96        14.01         9.96         8.02        20.05        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       22.65        20.58        20.19        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       13.71        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
        2.86        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       10.09        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 
       47.05        19.00         2.99        14.96        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       21.99        26.01        25.02        24.00         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 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-A44F TCGA-44-2656 
       97.74       120.79        37.71        49.05         4.37        46.98 
TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
       44.42        42.77        37.15        38.24        33.73        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 
       33.30        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       22.26        20.52        71.47        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       49.28         8.22         9.27        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
        3.91        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       10.13        36.99        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       35.21        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       40.73        15.25        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
       70.26        31.30        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
       22.03         3.91        23.15        25.41        15.39        18.64 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       34.19        17.65        18.44        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       15.19        23.08         5.06        17.79        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       29.19        22.16        15.42        17.56        15.72        14.47 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36        13.74        20.28        17.72        19.96        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
       17.10        17.62        14.66         1.58        12.33        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 
       21.40         3.25         0.92        15.81        19.99         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       39.98        42.38        14.60        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-64-5779 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-69-7760 TCGA-69-7761 
       14.04        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
       13.41        13.51        14.01        13.45         4.24        19.43 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        8.42         6.90        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       30.31         9.24         1.25        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 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        11.61        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        12.23        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
       23.61         1.08        19.00        41.82        18.67        12.39 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       27.29         2.76        19.89        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       61.48        25.48        18.54         0.59        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       20.58        21.44        19.76        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE 
       34.85        36.76         1.45        21.57        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       32.48        19.00        14.30        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       41.59        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.49         0.43        19.82        59.11 

  CHRND MUTATED CHRND WILD-TYPE 
           7.17            0.00 
  CHRND MUTATED CHRND WILD-TYPE 
         101.72          238.29 
  CHRND MUTATED CHRND WILD-TYPE 
          28.37           21.42 
[1] "7.2 - 101.7 (28.4)" "0.0 - 238.3 (21.4)"
[1] "hr=" "2.3"
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      117      126        45        64         68
                 vv
clus              STAGE IIIB STAGE IV
  CHRND MUTATED            0        1
  CHRND WILD-TYPE         11       23
D61V3, multiclass
            clus
vv           CHRND MUTATED CHRND WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             117
  STAGE IB               6             126
  STAGE IIA              1              45
  STAGE IIB              2              64
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              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
  CHRND MUTATED     3  11   2   0
  CHRND WILD-TYPE 153 250  41  18
D61V4, multiclass
    clus
vv   CHRND MUTATED CHRND WILD-TYPE
  T1             3             153
  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 297  86    70
D61V5, multiclass
       clus
vv      CHRND MUTATED CHRND WILD-TYPE
  N0               11             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"
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 256 209
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRND MUTATED      4   12
  CHRND WILD-TYPE  256  209
        clus
vv       CHRND MUTATED CHRND WILD-TYPE
  FEMALE             4             256
  MALE              12             209
[1] 2 2
[1] FALSE
D61V8, binary
                 cls
clus                0   1
  CHRND MUTATED    14   1
  CHRND WILD-TYPE 370  54
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRND MUTATED     14    1
  CHRND WILD-TYPE  370   54
     clus
vv    CHRND MUTATED CHRND WILD-TYPE
  NO             14             370
  YES             1              54
[1] 2 2
[1] FALSE
D61V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  CHRND MUTATED                            0                                 4
  CHRND WILD-TYPE                         17                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  CHRND MUTATED                                                    9
  CHRND WILD-TYPE                                                287
                 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                                      17
  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                                   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 300  12   4  25
D61V13, multiclass
    clus
vv   CHRND MUTATED CHRND WILD-TYPE
  R0            12             300
  R1             0              12
  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                        29   367
D61V14, multiclass
                                  clus
vv                                 CHRND MUTATED CHRND WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              29
  WHITE                                       11             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"
D61V15, binary
                 cls
clus                0   1
  CHRND MUTATED     0  12
  CHRND WILD-TYPE   6 339
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRND MUTATED      0   12
  CHRND WILD-TYPE    6  339
                        clus
vv                       CHRND MUTATED CHRND WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            12             339
[1] 2 2
[1] FALSE

Clustering(62) Variable = KLK1 MUTATION ANALYSIS
D62V1, survival
                sevent
clus2              0   1
  KLK1 MUTATED     6   2
  KLK1 WILD-TYPE 292 169
  KLK1 MUTATED KLK1 WILD-TYPE 
             8            461 
  KLK1 MUTATED KLK1 WILD-TYPE 
             2            169 
$`KLK1 MUTATED`
TCGA-50-5935 TCGA-05-4390 TCGA-53-A4EZ TCGA-55-6968 TCGA-62-8399 TCGA-69-7765 
       21.47        37.02        35.21        42.51        88.64         5.42 
TCGA-69-7978 TCGA-86-8673 
        4.41        28.34 

$`KLK1 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-6597 TCGA-55-1592 
       16.04        17.16        11.64        40.60        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4395 
        2.43        10.09        50.07         3.98        45.01         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         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-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       55.33        22.26        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       53.16        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       34.29        30.54        13.94        30.58        14.30        80.52 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
        5.62        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
      107.21        70.26        31.30        28.67        20.02        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
       32.71        22.03         3.91        23.15        25.41        15.39 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       18.64        11.28        34.19        17.65        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       29.23        29.72        15.19        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.72        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       19.96        26.01        17.10        17.62        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       12.33        20.71        21.40         3.25         0.92        15.81 
TCGA-55-A4DG TCGA-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-64-1679 
       13.61        39.25        40.96        29.92        56.81        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 
        4.64         6.64         6.12        22.68        13.61         7.56 
TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05        13.41        13.51        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       19.43         8.42         6.90        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 
        4.31        30.31         9.24         1.25        50.33        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       77.85        43.82        85.15        49.84        36.66       108.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
      100.57       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-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      238.29        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       26.01        39.35        10.55       232.18        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
      110.50        93.11        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 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 
       11.61        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-91-6840 TCGA-91-6847 TCGA-91-6848 
        1.97        10.19         2.60        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 
       17.46        23.61         1.08        19.00        41.82        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       12.39        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       21.60        20.58        21.44        19.76        20.84        18.67 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
       24.56        34.85        36.76         1.45        21.57        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 
       35.47        32.48        19.00        14.30        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        5.49        41.59        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       47.08         0.49         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         21.440 
[1] "4.4 - 88.6 (31.8)"  "0.0 - 238.3 (21.4)"
[1] "hr=" "1.8"
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      120      130        45        65         69
                vv
clus             STAGE IIIB STAGE IV
  KLK1 MUTATED            0        1
  KLK1 WILD-TYPE         11       23
D62V3, multiclass
            clus
vv           KLK1 MUTATED KLK1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            120
  STAGE IB              2            130
  STAGE IIA             1             45
  STAGE IIB             1             65
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              1             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 154 256  43  17
D62V4, multiclass
    clus
vv   KLK1 MUTATED KLK1 WILD-TYPE
  T1            2            154
  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 303  87    71
D62V5, multiclass
       clus
vv      KLK1 MUTATED KLK1 WILD-TYPE
  N0               5            303
  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 258 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLK1 MUTATED      2    6
  KLK1 WILD-TYPE  258  215
        clus
vv       KLK1 MUTATED KLK1 WILD-TYPE
  FEMALE            2            258
  MALE              6            215
[1] 2 2
[1] FALSE
D62V8, binary
                cls
clus               0   1
  KLK1 MUTATED     5   3
  KLK1 WILD-TYPE 379  52
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLK1 MUTATED      5    3
  KLK1 WILD-TYPE  379   52
     clus
vv    KLK1 MUTATED KLK1 WILD-TYPE
  NO             5            379
  YES            3             52
[1] 2 2
[1] FALSE
D62V9, continuous
[1] "Remove cluster labels:" "KLK1 MUTATED"          
clus
  KLK1 MUTATED KLK1 WILD-TYPE 
             2            120 
    TCGA-44-6147     TCGA-44-A47F     TCGA-49-6742     TCGA-55-7573 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-55-7725     TCGA-55-7914     TCGA-55-8205     TCGA-55-8511 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8621     TCGA-55-A491     TCGA-55-A492 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-64-1677     TCGA-73-4662     TCGA-73-7498     TCGA-93-8067 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-35-4122     TCGA-35-4123     TCGA-35-5375 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-44-3396     TCGA-44-3918     TCGA-44-4112     TCGA-44-6144 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-44-6775     TCGA-44-7660     TCGA-49-4486     TCGA-49-4494 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-49-4505     TCGA-49-4506     TCGA-49-4510     TCGA-49-6743 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-49-6744     TCGA-53-7624     TCGA-55-5899     TCGA-55-7283 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-55-7574     TCGA-55-7910     TCGA-55-7913     TCGA-55-7995 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-55-8089     TCGA-55-8096     TCGA-55-8208     TCGA-55-8507 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-55-8508     TCGA-55-8512     TCGA-55-8513     TCGA-55-8620 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A494     TCGA-62-8394 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-62-8395     TCGA-62-8397     TCGA-62-8398     TCGA-62-8402 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R     TCGA-62-A46S 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y     TCGA-62-A470 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-62-A471     TCGA-62-A472     TCGA-64-1681     TCGA-64-5775 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-64-5778     TCGA-69-7974     TCGA-69-8254     TCGA-71-6725 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     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-73-7499 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-75-5122     TCGA-83-5908     TCGA-86-6562     TCGA-86-6851 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-86-7701     TCGA-86-7711     TCGA-86-7713     TCGA-86-7714 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-86-7953     TCGA-86-7954     TCGA-86-7955     TCGA-86-8054 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-86-8055     TCGA-86-8056     TCGA-86-8073     TCGA-86-8074 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-86-8075     TCGA-86-8076     TCGA-86-8278     TCGA-86-8279 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-86-8280     TCGA-86-8281     TCGA-86-8358     TCGA-86-8359 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-86-8668     TCGA-86-8669     TCGA-86-8671     TCGA-86-A456 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6829     TCGA-91-6849 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-93-7347     TCGA-93-7348     TCGA-93-A4JN     TCGA-93-A4JO 
"KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" "KLK1 WILD-TYPE" 
    TCGA-95-7567     TCGA-99-7458     TCGA-MN-A4N4     TCGA-MN-A4N5 
"KLK1 WILD-TYPE" "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                         16                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KLK1 MUTATED                                                    2
  KLK1 WILD-TYPE                                                294
                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                                     16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            294
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                  18
  LUNG CLEAR CELL ADENOCARCINOMA                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                              3
  LUNG MUCINOUS ADENOCARCINOMA                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                  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 309  12   4  24
D62V13, multiclass
    clus
vv   KLK1 MUTATED KLK1 WILD-TYPE
  R0            3            309
  R1            0             12
  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                        29   372
D62V14, multiclass
                                  clus
vv                                 KLK1 MUTATED KLK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             29
  WHITE                                       6            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"
D62V15, binary
                cls
clus               0   1
  KLK1 MUTATED     1   6
  KLK1 WILD-TYPE   5 345
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLK1 MUTATED      1    6
  KLK1 WILD-TYPE    5  345
                        clus
vv                       KLK1 MUTATED KLK1 WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO            6            345
[1] 2 2
[1] FALSE

Clustering(63) Variable = KLHL5 MUTATION ANALYSIS
D63V1, survival
                 sevent
clus2               0   1
  KLHL5 MUTATED    10   4
  KLHL5 WILD-TYPE 288 167
  KLHL5 MUTATED KLHL5 WILD-TYPE 
             14             455 
  KLHL5 MUTATED KLHL5 WILD-TYPE 
              4             167 
$`KLHL5 MUTATED`
TCGA-44-7661 TCGA-55-7284 TCGA-91-6836 TCGA-95-7947 TCGA-95-A4VN TCGA-44-2657 
       18.31         7.99        13.71        15.68        18.18        44.42 
TCGA-44-3918 TCGA-44-8120 TCGA-44-A4SS TCGA-49-4486 TCGA-55-A4DG TCGA-69-8255 
       34.06         8.55        13.64        76.21        19.99         4.24 
TCGA-86-7711 TCGA-NJ-A4YQ 
       34.39        47.08 

$`KLHL5 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
       48.62         5.79         7.79        16.01        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       21.44         6.15        19.66        19.73        17.98        16.93 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       19.69        32.12        18.15        13.68        16.93        22.65 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       20.58        19.59        20.19        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       16.18         1.45         6.12        17.29        16.54         2.86 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       15.65        21.40        17.92        20.19        20.52        17.75 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       20.68        24.30        23.80         6.35        10.09        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
        5.29        31.23         2.43        10.09        50.07         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
       45.01        37.02         0.00        24.03        47.05        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       26.01        25.02        25.02        24.00         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 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-38-4632 TCGA-38-A44F 
       97.74       120.79        37.71        49.05        44.61         4.37 
TCGA-44-2656 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
       46.98        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-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       19.46         7.17        36.07        18.87        23.64        12.66 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU TCGA-49-4487 
       15.98        15.32         9.44        11.54        13.45        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 
       29.46        29.75        55.89        53.29        55.33        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       49.28         8.22         9.27        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
        3.91        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99        36.79        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       13.94        35.21        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
      107.21        70.26        31.30        28.67        20.02        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
       32.71        22.03         3.91        23.15        25.41        15.39 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       18.64        11.28        34.19        17.65        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       29.23        29.72        15.19        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.72        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       19.96        26.01        17.10        17.62        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       12.33        20.71        21.40         3.25         0.92        15.81 
TCGA-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-64-1679 
       13.61        39.25        40.96        29.92        56.81        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41        13.41        13.51        14.01 
TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 
       13.45        19.43         8.42         6.90        23.38        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-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 
       66.64        77.85        43.82        85.15        49.84        36.66 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
      108.66       100.57       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      104.19       238.29        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
       53.33        26.01        39.35        10.55       232.18        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59       110.50        93.11        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       31.13        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 
       11.61        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-91-6840 TCGA-91-6847 
       41.36         1.97        10.19         2.60        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
        7.36         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       22.45        17.46        23.61         1.08        19.00        41.82 
TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 
       18.67        12.39        27.29         2.76        19.89        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        61.48        25.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       15.91        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       14.30        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 
       18.08        35.47        32.48        19.00        14.30        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.85         5.49        41.59        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        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64         0.49         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 
         18.245          21.570 
[1] "4.2 - 76.2 (18.2)"  "0.0 - 238.3 (21.6)"
[1] "hr=" "1.1"
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      114      128        44        65         70
                 vv
clus              STAGE IIIB STAGE IV
  KLHL5 MUTATED            0        0
  KLHL5 WILD-TYPE         11       24
D63V3, multiclass
            clus
vv           KLHL5 MUTATED KLHL5 WILD-TYPE
  STAGE I                0               4
  STAGE IA               7             114
  STAGE IB               4             128
  STAGE IIA              2              44
  STAGE IIB              1              65
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               0              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
  KLHL5 MUTATED     7   6   1   0
  KLHL5 WILD-TYPE 149 255  42  18
D63V4, multiclass
    clus
vv   KLHL5 MUTATED KLHL5 WILD-TYPE
  T1             7             149
  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 297  87    72
D63V5, multiclass
       clus
vv      KLHL5 MUTATED KLHL5 WILD-TYPE
  N0               11             297
  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 254 213
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL5 MUTATED      6    8
  KLHL5 WILD-TYPE  254  213
        clus
vv       KLHL5 MUTATED KLHL5 WILD-TYPE
  FEMALE             6             254
  MALE               8             213
[1] 2 2
[1] FALSE
D63V8, binary
                 cls
clus                0   1
  KLHL5 MUTATED    14   0
  KLHL5 WILD-TYPE 370  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL5 MUTATED     14    0
  KLHL5 WILD-TYPE  370   55
     clus
vv    KLHL5 MUTATED KLHL5 WILD-TYPE
  NO             14             370
  YES             0              55
[1] 2 2
[1] FALSE
D63V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  KLHL5 MUTATED                            0                                 1
  KLHL5 WILD-TYPE                         17                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  KLHL5 MUTATED                                                   10
  KLHL5 WILD-TYPE                                                286
                 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                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  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                    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 304  12   4  24
D63V13, multiclass
    clus
vv   KLHL5 MUTATED KLHL5 WILD-TYPE
  R0             8             304
  R1             0              12
  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                        29   365
D63V14, multiclass
                                  clus
vv                                 KLHL5 MUTATED KLHL5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              29
  WHITE                                       13             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"
D63V15, binary
                 cls
clus                0   1
  KLHL5 MUTATED     2  12
  KLHL5 WILD-TYPE   4 339
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL5 MUTATED      2   12
  KLHL5 WILD-TYPE    4  339
                        clus
vv                       KLHL5 MUTATED KLHL5 WILD-TYPE
  HISPANIC OR LATINO                 2               4
  NOT HISPANIC OR LATINO            12             339
[1] 2 2
[1] FALSE

Clustering(64) Variable = DSC2 MUTATION ANALYSIS
D64V1, survival
                sevent
clus2              0   1
  DSC2 MUTATED    14   6
  DSC2 WILD-TYPE 284 165
  DSC2 MUTATED DSC2 WILD-TYPE 
            20            449 
  DSC2 MUTATED DSC2 WILD-TYPE 
             6            165 
$`DSC2 MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-44-7670 TCGA-49-6742 TCGA-55-8207 TCGA-MP-A4TC 
       19.96        14.01        29.00        16.04        32.12         2.43 
TCGA-44-2657 TCGA-44-7662 TCGA-49-6743 TCGA-53-7626 TCGA-55-7576 TCGA-55-8507 
       44.42         7.17        53.29        30.54        22.03        13.74 
TCGA-55-8508 TCGA-69-A59K TCGA-78-7542 TCGA-86-8073 TCGA-97-7554 TCGA-97-7938 
       20.28        19.43        10.55        24.33        25.48         0.59 
TCGA-NJ-A4YI TCGA-NJ-A4YP 
        0.13         1.64 

$`DSC2 WILD-TYPE`
TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 
        9.96         8.02        20.05         9.01        26.01        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       15.02        28.41        35.28        11.64        14.73        26.30 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 
       38.10        23.93        27.78        86.01        18.31        29.23 
TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 
        9.37        11.08        46.72        17.16        11.64        40.60 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 
       21.47        41.69        23.05        48.62         5.79         7.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 
        7.99        16.01        23.18        14.53        21.44         6.15 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8511 
       19.66        19.73        17.98        16.93        19.69        18.15 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF 
       13.68        16.93        22.65        20.58        19.59        20.19 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       20.65        13.87        52.60        82.68        39.09         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
       50.24        10.55        85.32        13.71        16.18         1.45 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
        6.12        17.29        16.54         2.86        15.68        15.65 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       21.40        18.18        17.92        20.19        20.52        17.75 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       20.68        24.30        23.80         6.35        10.09        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 
        5.29        31.23        10.09        50.07         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       37.02         0.00        24.03        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        24.00         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-38-4632 TCGA-38-A44F TCGA-44-2656 
      120.79        37.71        49.05        44.61         4.37        46.98 
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-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
       19.46        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 
       32.84         8.81        29.46        29.75        55.89        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        48.46        60.72        57.53        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99        36.79        27.25        34.29 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       13.94        35.21        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
      107.21        70.26        31.30        28.67        20.02        27.09 
TCGA-55-7574 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
       32.71         3.91        23.15        25.41        15.39        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 
       11.28        34.19        17.65        18.44        19.82        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       29.72        15.19        23.08         5.06        17.79        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       15.65        29.19        22.16        15.42        17.56        15.72 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       14.47         0.36        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.62        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        3.25         0.92        15.81        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 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-69-7760 
       18.84        14.04        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41        13.41        13.51        14.01        13.45         4.24 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        8.42         6.90        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       30.31         9.24         1.25        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
       39.35       232.18        39.75        77.59       110.50        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 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        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
        1.08        19.00        41.82        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
       18.54        15.91        18.67         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.57        18.08        35.47        32.48        19.00        14.30 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       47.08         0.49         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 
        19.695         21.570 
[1] "0.1 - 53.3 (19.7)"  "0.0 - 238.3 (21.6)"
[1] "hr=" "1.3"
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      119      124        42        65         65
                vv
clus             STAGE IIIB STAGE IV
  DSC2 MUTATED            0        0
  DSC2 WILD-TYPE         11       24
D64V3, multiclass
            clus
vv           DSC2 MUTATED DSC2 WILD-TYPE
  STAGE I               0              4
  STAGE IA              2            119
  STAGE IB              8            124
  STAGE IIA             4             42
  STAGE IIB             1             65
  STAGE IIIA            5             65
  STAGE IIIB            0             11
  STAGE IV              0             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
  DSC2 MUTATED     6  13   1   0
  DSC2 WILD-TYPE 150 248  42  18
D64V4, multiclass
    clus
vv   DSC2 MUTATED DSC2 WILD-TYPE
  T1            6            150
  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 298  85    67
D64V5, multiclass
       clus
vv      DSC2 MUTATED DSC2 WILD-TYPE
  N0              10            298
  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 251 210
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED      9   11
  DSC2 WILD-TYPE  251  210
        clus
vv       DSC2 MUTATED DSC2 WILD-TYPE
  FEMALE            9            251
  MALE             11            210
[1] 2 2
[1] FALSE
D64V8, binary
                cls
clus               0   1
  DSC2 MUTATED    17   2
  DSC2 WILD-TYPE 367  53
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED     17    2
  DSC2 WILD-TYPE  367   53
     clus
vv    DSC2 MUTATED DSC2 WILD-TYPE
  NO            17            367
  YES            2             53
[1] 2 2
[1] FALSE
D64V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DSC2 MUTATED                            1                                 3
  DSC2 WILD-TYPE                         16                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DSC2 MUTATED                                                    8
  DSC2 WILD-TYPE                                                288
                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                                     16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            288
  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 299  12   4  24
D64V13, multiclass
    clus
vv   DSC2 MUTATED DSC2 WILD-TYPE
  R0           13            299
  R1            0             12
  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                        27   363
D64V14, multiclass
                                  clus
vv                                 DSC2 MUTATED DSC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   3             27
  WHITE                                      15            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"
D64V15, binary
                cls
clus               0   1
  DSC2 MUTATED     1  14
  DSC2 WILD-TYPE   5 337
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED      1   14
  DSC2 WILD-TYPE    5  337
                        clus
vv                       DSC2 MUTATED DSC2 WILD-TYPE
  HISPANIC OR LATINO                1              5
  NOT HISPANIC OR LATINO           14            337
[1] 2 2
[1] FALSE

Clustering(65) Variable = RNF160 MUTATION ANALYSIS
D65V1, survival
                  sevent
clus2                0   1
  RNF160 MUTATED     9   6
  RNF160 WILD-TYPE 289 165
  RNF160 MUTATED RNF160 WILD-TYPE 
              15              454 
  RNF160 MUTATED RNF160 WILD-TYPE 
               6              165 
$`RNF160 MUTATED`
TCGA-05-4382 TCGA-55-8090 TCGA-MP-A4TC TCGA-05-4390 TCGA-35-5375 TCGA-44-8117 
       19.96        19.66         2.43        37.02         8.68        12.66 
TCGA-53-7624 TCGA-67-3771 TCGA-86-8673 TCGA-86-A4JF TCGA-95-7567 TCGA-97-7554 
       34.29        20.05        28.34        24.23        18.67        25.48 
TCGA-97-8174 TCGA-MN-A4N4 TCGA-MP-A4TF 
        5.39        38.63        11.05 

$`RNF160 WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       14.01         9.96         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       14.53        21.44         6.15        19.73        17.98        16.93 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       19.69        32.12        18.15        13.68        16.93        22.65 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       20.58        19.59        20.19        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       13.71        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD 
        6.35        10.09        27.19         5.29        31.23        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 
       50.07         3.98        45.01         0.00        24.03        47.05 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       19.00         2.99        14.96        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 
       21.99        26.01        25.02        25.02        24.00         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 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-38-4632 TCGA-38-A44F 
       97.74       120.79        37.71        49.05        44.61         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       46.98        44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       19.56        23.15        21.63        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        22.72        19.46         7.17        36.07        18.87 
TCGA-44-7672 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       23.64         8.55        15.98        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       35.54        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       55.89        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 
      101.72        15.72        60.16        47.41        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        9.27        14.27        78.67         8.45        15.12        48.46 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       60.72        57.53        53.16        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05        12.16         6.21         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 
       36.79        27.25        30.54        13.94        35.21        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       14.30        80.52         5.62        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       46.03        53.65         3.88        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       92.81        24.99        40.54       107.21        70.26        31.30 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
       28.67        20.02        27.09        32.71        22.03         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
       23.15        25.41        15.39        18.64        11.28        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       23.08         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       13.74        20.28        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.62        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        3.25         0.92        15.81        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-67-3772 
        2.04        42.90        28.41        51.25        28.47        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
       14.04        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
       13.41        13.51        14.01        13.45         4.24        19.43 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        8.42         6.90        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       30.31         9.24         1.25        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 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        11.61 
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-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
        1.08        19.00        41.82        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 
       19.89        42.25        64.60        63.52        61.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
        0.59        15.91        18.67        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       14.30        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N5 
       18.08        35.47        32.48        19.00        14.30         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        5.49        41.59        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        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.49         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            21.52 
[1] "2.4 - 38.6 (20.0)"  "0.0 - 238.3 (21.5)"
[1] "hr=" "1.7"
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      118      128        44        64         67
                  vv
clus               STAGE IIIB STAGE IV
  RNF160 MUTATED            0        1
  RNF160 WILD-TYPE         11       23
D65V3, multiclass
            clus
vv           RNF160 MUTATED RNF160 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              118
  STAGE IB                4              128
  STAGE IIA               2               44
  STAGE IIB               2               64
  STAGE IIIA              3               67
  STAGE IIIB              0               11
  STAGE IV                1               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
  RNF160 MUTATED     4  10   1   0
  RNF160 WILD-TYPE 152 251  42  18
D65V4, multiclass
    clus
vv   RNF160 MUTATED RNF160 WILD-TYPE
  T1              4              152
  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 297  88    69
D65V5, multiclass
       clus
vv      RNF160 MUTATED RNF160 WILD-TYPE
  N0                11              297
  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 254 212
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF160 MUTATED      6    9
  RNF160 WILD-TYPE  254  212
        clus
vv       RNF160 MUTATED RNF160 WILD-TYPE
  FEMALE              6              254
  MALE                9              212
[1] 2 2
[1] FALSE
D65V8, binary
                  cls
clus                 0   1
  RNF160 MUTATED    12   1
  RNF160 WILD-TYPE 372  54
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF160 MUTATED     12    1
  RNF160 WILD-TYPE  372   54
     clus
vv    RNF160 MUTATED RNF160 WILD-TYPE
  NO              12              372
  YES              1               54
[1] 2 2
[1] FALSE
D65V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RNF160 MUTATED                            0                                 3
  RNF160 WILD-TYPE                         17                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RNF160 MUTATED                                                    9
  RNF160 WILD-TYPE                                                287
                  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                                       17
  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                                    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 300  12   4  25
D65V13, multiclass
    clus
vv   RNF160 MUTATED RNF160 WILD-TYPE
  R0             12              300
  R1              0               12
  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                        29   366
D65V14, multiclass
                                  clus
vv                                 RNF160 MUTATED RNF160 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               29
  WHITE                                        12              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"
D65V15, binary
                  cls
clus                 0   1
  RNF160 MUTATED     1  12
  RNF160 WILD-TYPE   5 339
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF160 MUTATED      1   12
  RNF160 WILD-TYPE    5  339
                        clus
vv                       RNF160 MUTATED RNF160 WILD-TYPE
  HISPANIC OR LATINO                  1                5
  NOT HISPANIC OR LATINO             12              339
[1] 2 2
[1] FALSE

Clustering(66) Variable = AIFM1 MUTATION ANALYSIS
D66V1, survival
                 sevent
clus2               0   1
  AIFM1 MUTATED     7   4
  AIFM1 WILD-TYPE 291 167
  AIFM1 MUTATED AIFM1 WILD-TYPE 
             11             458 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
              4             167 
$`AIFM1 MUTATED`
TCGA-38-4631 TCGA-55-A48X TCGA-95-7043 TCGA-44-6774 TCGA-50-6594 TCGA-55-8506 
       11.64        22.65        16.54        21.63        12.16         0.36 
TCGA-55-A494 TCGA-69-7974 TCGA-86-A456 TCGA-86-A4P7 TCGA-97-7938 
       15.81         6.05        29.46        13.64         0.59 

$`AIFM1 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 
       26.01        15.02        15.02        28.41        35.28        14.73 
TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       20.58        19.59        20.19        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 
       13.71        16.18         1.45         6.12        17.29         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       15.68        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       10.09        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       47.05        19.00         2.99        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-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-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 
       44.61         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-44-6148 TCGA-44-6775 TCGA-44-6777 
       28.01        23.77        19.56        23.15        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
       61.28        16.44        22.72        19.46         7.17        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       18.87        23.64        12.66         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
        9.44        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 
       29.46        29.75        55.89        53.29        55.33        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       49.28         8.22         9.27        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
        3.91        25.55        11.05         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99        36.79        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       35.21        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       40.73        15.25        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
       70.26        31.30        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
       22.03         3.91        23.15        25.41        15.39        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 
       11.28        34.19        17.65        18.44        19.82        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       29.72        15.19        23.08         5.06        17.79        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       15.65        29.19        22.16        15.42        17.56        15.72 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
       14.47        13.74        20.28        17.72        19.96        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
       17.10        17.62        14.66         1.58        12.33        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
       21.40         3.25         0.92        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-69-7760 
       18.84        14.04        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 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 
       13.41        13.51        14.01        13.45         4.24        19.43 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        8.42         6.90        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       30.31         9.24         1.25        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 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        11.61 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-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-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
        1.08        19.00        41.82        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       25.48        18.54        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       15.39        16.41        14.30        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       19.76        20.84        18.67        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        1.45        21.57        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       14.30        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE 
       37.35        86.04        58.85         5.49        41.59        29.46 
TCGA-MP-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 
       74.33         0.13         1.64        47.08         0.49         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          21.585 
[1] "0.4 - 29.5 (13.6)"  "0.0 - 238.3 (21.6)"
[1] "hr=" "2.4"
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      118      128        45        65         67
                 vv
clus              STAGE IIIB STAGE IV
  AIFM1 MUTATED            0        0
  AIFM1 WILD-TYPE         11       24
D66V3, multiclass
            clus
vv           AIFM1 MUTATED AIFM1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               3             118
  STAGE IB               4             128
  STAGE IIA              1              45
  STAGE IIB              1              65
  STAGE IIIA             3              67
  STAGE IIIB             0              11
  STAGE IV               0              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
  AIFM1 MUTATED     5   5   2   0
  AIFM1 WILD-TYPE 151 256  41  18
D66V4, multiclass
    clus
vv   AIFM1 MUTATED AIFM1 WILD-TYPE
  T1             5             151
  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 300  88    69
D66V5, multiclass
       clus
vv      AIFM1 MUTATED AIFM1 WILD-TYPE
  N0                8             300
  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 248 221
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED     12    0
  AIFM1 WILD-TYPE  248  221
        clus
vv       AIFM1 MUTATED AIFM1 WILD-TYPE
  FEMALE            12             248
  MALE               0             221
[1] 2 2
[1] FALSE
D66V8, binary
                 cls
clus                0   1
  AIFM1 MUTATED     9   2
  AIFM1 WILD-TYPE 375  53
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED      9    2
  AIFM1 WILD-TYPE  375   53
     clus
vv    AIFM1 MUTATED AIFM1 WILD-TYPE
  NO              9             375
  YES             2              53
[1] 2 2
[1] FALSE
D66V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  AIFM1 MUTATED                            0                                 2
  AIFM1 WILD-TYPE                         17                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AIFM1 MUTATED                                                    8
  AIFM1 WILD-TYPE                                                288
                 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                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  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                                   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 304  12   4  25
D66V13, multiclass
    clus
vv   AIFM1 MUTATED AIFM1 WILD-TYPE
  R0             8             304
  R1             0              12
  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                        29   369
D66V14, multiclass
                                  clus
vv                                 AIFM1 MUTATED AIFM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    1              29
  WHITE                                        9             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"
D66V15, binary
                 cls
clus                0   1
  AIFM1 MUTATED     0  11
  AIFM1 WILD-TYPE   6 340
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED      0   11
  AIFM1 WILD-TYPE    6  340
                        clus
vv                       AIFM1 MUTATED AIFM1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            11             340
[1] 2 2
[1] FALSE

Clustering(67) Variable = DOT1L MUTATION ANALYSIS
D67V1, survival
                 sevent
clus2               0   1
  DOT1L MUTATED     8   5
  DOT1L WILD-TYPE 290 166
  DOT1L MUTATED DOT1L WILD-TYPE 
             13             456 
  DOT1L MUTATED DOT1L WILD-TYPE 
              5             166 
$`DOT1L MUTATED`
TCGA-05-4384 TCGA-55-8511 TCGA-91-6836 TCGA-49-4486 TCGA-49-6767 TCGA-50-5072 
       14.01        18.15        13.71        76.21        22.26         8.22 
TCGA-53-7624 TCGA-55-7727 TCGA-62-8395 TCGA-64-5781 TCGA-69-7974 TCGA-78-7156 
       34.29         3.91        39.98        51.25         6.05        32.09 
TCGA-86-A4JF 
       24.23 

$`DOT1L WILD-TYPE`
TCGA-05-4382 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96         9.96         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       16.93        19.69        32.12        13.68        16.93        22.65 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       20.58        19.59        20.19        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       16.18         1.45         6.12        17.29        16.54         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       15.68        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       10.09        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       47.05        19.00         2.99        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-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-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 
       44.61         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-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 
       15.32         9.44        11.54        13.64        13.45        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-50-5044 
       29.46        29.75        55.89        53.29        55.33        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47       101.72        15.72        60.16        47.41        49.28 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        9.27        14.27        78.67         8.45        15.12        48.46 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       60.72        57.53        53.16        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05        12.16         6.21         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 
       36.79        27.25        30.54        13.94        35.21        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       14.30        80.52         5.62        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       46.03        53.65         3.88        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       92.81        24.99        40.54       107.21        70.26        31.30 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7728 
       28.67        20.02        27.09        32.71        22.03        23.15 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       25.41        15.39        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.44        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42        17.56        15.72        14.47         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       14.66         1.58        12.33        20.71        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 
        0.92        15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       56.81        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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        5.42         7.56         4.41        13.41        13.51        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 
       13.45         4.24        19.43         8.42         6.90        23.38 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
       50.33        66.64        77.85        43.82        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       36.66       108.66       100.57       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 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-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      104.19       238.29        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
       53.33        26.01        39.35        10.55       232.18        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59       110.50        93.11        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        38.04        20.55        32.78        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       35.24        37.74         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       22.82        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60        11.61        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-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-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
        7.36         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       22.45        17.46        23.61         1.08        19.00        41.82 
TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 
       18.67        12.39        27.29         2.76        19.89        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        61.48        25.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       15.91        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       14.30        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 
       18.08        35.47        32.48        19.00        14.30        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.85         5.49        41.59        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        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        47.08         0.49         0.43        19.82        59.11 

  DOT1L MUTATED DOT1L WILD-TYPE 
           3.91            0.00 
  DOT1L MUTATED DOT1L WILD-TYPE 
          76.21          238.29 
  DOT1L MUTATED DOT1L WILD-TYPE 
         22.260          21.455 
[1] "3.9 - 76.2 (22.3)"  "0.0 - 238.3 (21.5)"
[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      120      128        46        63         66
                 vv
clus              STAGE IIIB STAGE IV
  DOT1L MUTATED            0        2
  DOT1L WILD-TYPE         11       22
D67V3, multiclass
            clus
vv           DOT1L MUTATED DOT1L WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             120
  STAGE IB               4             128
  STAGE IIA              0              46
  STAGE IIB              3              63
  STAGE IIIA             4              66
  STAGE IIIB             0              11
  STAGE IV               2              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
  DOT1L MUTATED     2   8   3   1
  DOT1L WILD-TYPE 154 253  40  17
D67V4, multiclass
    clus
vv   DOT1L MUTATED DOT1L WILD-TYPE
  T1             2             154
  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 299  88    68
D67V5, multiclass
       clus
vv      DOT1L MUTATED DOT1L WILD-TYPE
  N0                9             299
  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 253 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOT1L MUTATED      7    7
  DOT1L WILD-TYPE  253  214
        clus
vv       DOT1L MUTATED DOT1L WILD-TYPE
  FEMALE             7             253
  MALE               7             214
[1] 2 2
[1] FALSE
D67V8, binary
                 cls
clus                0   1
  DOT1L MUTATED     9   3
  DOT1L WILD-TYPE 375  52
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOT1L MUTATED      9    3
  DOT1L WILD-TYPE  375   52
     clus
vv    DOT1L MUTATED DOT1L WILD-TYPE
  NO              9             375
  YES             3              52
[1] 2 2
[1] FALSE
D67V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DOT1L MUTATED                            0                                 6
  DOT1L WILD-TYPE                         17                                96
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DOT1L MUTATED                                                    8
  DOT1L WILD-TYPE                                                288
                 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                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               96
  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"
D67V11, continuous
D67V12, continuous
                 vv
clus               R0  R1  R2  RX
  DOT1L MUTATED     9   0   0   2
  DOT1L WILD-TYPE 303  12   4  23
D67V13, multiclass
    clus
vv   DOT1L MUTATED DOT1L WILD-TYPE
  R0             9             303
  R1             0              12
  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                        30   366
D67V14, multiclass
                                  clus
vv                                 DOT1L MUTATED DOT1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              30
  WHITE                                       12             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"
D67V15, binary
                 cls
clus                0   1
  DOT1L MUTATED     1   9
  DOT1L WILD-TYPE   5 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOT1L MUTATED      1    9
  DOT1L WILD-TYPE    5  342
                        clus
vv                       DOT1L MUTATED DOT1L WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO             9             342
[1] 2 2
[1] FALSE

Clustering(68) Variable = MCM9 MUTATION ANALYSIS
D68V1, survival
                sevent
clus2              0   1
  MCM9 MUTATED     2   1
  MCM9 WILD-TYPE 296 170
  MCM9 MUTATED MCM9 WILD-TYPE 
             3            466 
  MCM9 MUTATED MCM9 WILD-TYPE 
             1            170 
$`MCM9 MUTATED`
TCGA-38-4625 TCGA-49-4486 TCGA-69-7979 
       97.74        76.21        13.41 

$`MCM9 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       17.29        16.54         2.86        15.68        15.65        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       18.18        17.92        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 
       24.30        23.80         6.35        10.09        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 
       31.23         2.43        10.09        50.07         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       37.02         0.00        24.03        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        24.00         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-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       37.71        49.05        44.61         4.37        46.98        44.42 
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-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       19.46         7.17        36.07        18.87        23.64        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
        8.55        15.98        15.32         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       13.45        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       55.33        22.26        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       53.16        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 
       34.29        30.54        13.94        35.21        30.58        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       80.52         5.62        42.51        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       53.65         3.88        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26        31.30        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       20.02        27.09        32.71        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       25.41        15.39        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.44        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42        17.56        15.72        14.47         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       14.66         1.58        12.33        20.71        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       29.92        56.81        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-69-7760 TCGA-69-7761 
       14.04        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       13.51        14.01        13.45         4.24        19.43         8.42 
TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        6.90        23.38        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
        9.24         1.25        50.33        66.64        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       85.15        49.84        36.66       108.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 
       64.90        22.92         9.57       104.19       238.29        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
       10.55       232.18        39.75        77.59       110.50        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 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        11.61        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        12.23        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
       23.61         1.08        19.00        41.82        18.67        12.39 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       27.29         2.76        19.89        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       61.48        25.48        18.54         0.59        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       20.58        21.44        19.76        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE 
       34.85        36.76         1.45        21.57        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       32.48        19.00        14.30        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       41.59        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.49         0.43        19.82        59.11 

  MCM9 MUTATED MCM9 WILD-TYPE 
         13.41           0.00 
  MCM9 MUTATED MCM9 WILD-TYPE 
         97.74         238.29 
  MCM9 MUTATED MCM9 WILD-TYPE 
        76.210         21.455 
[1] "13.4 - 97.7 (76.2)" "0.0 - 238.3 (21.5)"
[1] "hr=" "2.5"
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      120      130        46        66         70
                vv
clus             STAGE IIIB STAGE IV
  MCM9 MUTATED            0        0
  MCM9 WILD-TYPE         11       24
D68V3, multiclass
            clus
vv           MCM9 MUTATED MCM9 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            120
  STAGE IB              2            130
  STAGE IIA             0             46
  STAGE IIB             0             66
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             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
  MCM9 MUTATED     1   2   0   0
  MCM9 WILD-TYPE 155 259  43  18
D68V4, multiclass
    clus
vv   MCM9 MUTATED MCM9 WILD-TYPE
  T1            1            155
  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 305  89    72
D68V5, multiclass
       clus
vv      MCM9 MUTATED MCM9 WILD-TYPE
  N0               3            305
  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 258 220
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      2    1
  MCM9 WILD-TYPE  258  220
        clus
vv       MCM9 MUTATED MCM9 WILD-TYPE
  FEMALE            2            258
  MALE              1            220
[1] 2 2
[1] FALSE
D68V8, binary
                cls
clus               0   1
  MCM9 MUTATED     3   0
  MCM9 WILD-TYPE 381  55
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      3    0
  MCM9 WILD-TYPE  381   55
     clus
vv    MCM9 MUTATED MCM9 WILD-TYPE
  NO             3            381
  YES            0             55
[1] 2 2
[1] FALSE
D68V9, continuous
[1] "Remove cluster labels:" "MCM9 MUTATED"          
clus
  MCM9 MUTATED MCM9 WILD-TYPE 
             1            121 
    TCGA-44-6147     TCGA-44-A47F     TCGA-49-6742     TCGA-55-7573 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-7725     TCGA-55-7914     TCGA-55-8205     TCGA-55-8511 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8621     TCGA-55-A491     TCGA-55-A492 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-64-1677     TCGA-73-4662     TCGA-73-7498     TCGA-93-8067 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-35-4122     TCGA-35-4123     TCGA-35-5375 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-44-3396     TCGA-44-3918     TCGA-44-4112     TCGA-44-6144 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-44-6775     TCGA-44-7660     TCGA-49-4494     TCGA-49-4505 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-49-4506     TCGA-49-4510     TCGA-49-6743     TCGA-49-6744 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-53-7624     TCGA-53-A4EZ     TCGA-55-5899     TCGA-55-7283 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-7574     TCGA-55-7910     TCGA-55-7913     TCGA-55-7995 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8089     TCGA-55-8096     TCGA-55-8208     TCGA-55-8507 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8508     TCGA-55-8512     TCGA-55-8513     TCGA-55-8620 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A494     TCGA-62-8394 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-62-8395     TCGA-62-8397     TCGA-62-8398     TCGA-62-8399 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-62-8402     TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-62-A46S     TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-62-A470     TCGA-62-A471     TCGA-62-A472     TCGA-64-1681 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-64-5775     TCGA-64-5778     TCGA-69-7974     TCGA-69-8254 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-71-6725     TCGA-71-8520     TCGA-73-4659     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-73-7499     TCGA-75-5122     TCGA-83-5908     TCGA-86-6562 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-6851     TCGA-86-7701     TCGA-86-7711     TCGA-86-7713 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-7714     TCGA-86-7953     TCGA-86-7954     TCGA-86-7955 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-8054     TCGA-86-8055     TCGA-86-8056     TCGA-86-8073 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-8074     TCGA-86-8075     TCGA-86-8076     TCGA-86-8278 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-8279     TCGA-86-8280     TCGA-86-8281     TCGA-86-8358 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8668     TCGA-86-8669     TCGA-86-8671 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6829 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-91-6849     TCGA-93-7347     TCGA-93-7348     TCGA-93-A4JN 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-93-A4JO     TCGA-95-7567     TCGA-99-7458     TCGA-MN-A4N4 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-MN-A4N5 
"MCM9 WILD-TYPE" 
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  MCM9 MUTATED                            1                                 0
  MCM9 WILD-TYPE                         16                               102
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MCM9 MUTATED                                                    2
  MCM9 WILD-TYPE                                                294
                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                                     16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                             102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            294
  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 310  12   4  25
D68V13, multiclass
[1] "Remove cluster labels:" "MCM9 MUTATED"          
clus
  MCM9 MUTATED MCM9 WILD-TYPE 
             2            351 
    TCGA-05-4382     TCGA-05-4384     TCGA-05-4396     TCGA-05-4402 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-4405     TCGA-05-4410     TCGA-05-4418     TCGA-05-4427 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-4434     TCGA-05-5420     TCGA-38-4629     TCGA-38-4630 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-38-4631     TCGA-38-6178     TCGA-38-7271     TCGA-44-2661 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-49-4501     TCGA-49-6742     TCGA-49-6761     TCGA-50-6597 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-1592     TCGA-55-7284     TCGA-55-7724     TCGA-55-7725 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-7726     TCGA-55-7914     TCGA-55-8090     TCGA-55-8091 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8203     TCGA-55-8204     TCGA-55-8205     TCGA-55-8207 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8511     TCGA-55-8619     TCGA-55-8621     TCGA-55-A48X 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-A491     TCGA-55-A492     TCGA-55-A4DF     TCGA-64-1677 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-67-6217     TCGA-73-4658     TCGA-73-4662     TCGA-73-7498 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-78-7166     TCGA-78-7633     TCGA-78-8660     TCGA-80-5607 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-80-5611     TCGA-93-8067     TCGA-93-A4JQ     TCGA-95-7562 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-95-7947     TCGA-95-7948     TCGA-95-A4VK     TCGA-95-A4VN 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-97-A4M2     TCGA-97-A4M7     TCGA-L9-A443     TCGA-L9-A444 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-MP-A4T8     TCGA-MP-A4TA     TCGA-MP-A4TC 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-MP-A4TD     TCGA-05-4244     TCGA-05-4249     TCGA-05-4250 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-4389     TCGA-05-4390     TCGA-05-4395     TCGA-05-4397 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-4398     TCGA-05-4403     TCGA-05-4415     TCGA-05-4417 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-4420     TCGA-05-4422     TCGA-05-4424     TCGA-05-4425 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-4426     TCGA-05-4430     TCGA-05-4432     TCGA-05-4433 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-5423     TCGA-05-5425     TCGA-05-5428     TCGA-05-5429 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-05-5715     TCGA-35-4122     TCGA-35-4123     TCGA-35-5375 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-38-4626     TCGA-38-4627     TCGA-38-4628     TCGA-38-4632 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-38-A44F     TCGA-44-2657     TCGA-44-2665     TCGA-44-3396 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-44-3398     TCGA-44-3918     TCGA-44-3919     TCGA-44-4112 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-44-6144     TCGA-44-6148     TCGA-44-6775     TCGA-44-A479 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-44-A47A     TCGA-44-A47B     TCGA-44-A47G     TCGA-44-A4SU 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-49-4487     TCGA-49-4488     TCGA-49-4494     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-49-6744     TCGA-49-6767     TCGA-50-5051 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-50-5055     TCGA-50-5066     TCGA-50-5931     TCGA-50-5942 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-50-5944     TCGA-50-6593     TCGA-50-6673     TCGA-50-8460 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-53-7624     TCGA-53-7626     TCGA-53-A4EZ     TCGA-55-5899 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-6642     TCGA-55-6712     TCGA-55-6970     TCGA-55-6971 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-6972     TCGA-55-6980     TCGA-55-6981     TCGA-55-6983 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-6985     TCGA-55-7227     TCGA-55-7281     TCGA-55-7570 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-7574     TCGA-55-7576     TCGA-55-7727     TCGA-55-7728 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-7815     TCGA-55-7903     TCGA-55-7907     TCGA-55-7910 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-7911     TCGA-55-7913     TCGA-55-7994     TCGA-55-7995 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8085     TCGA-55-8087     TCGA-55-8089     TCGA-55-8092 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8094     TCGA-55-8097     TCGA-55-8206     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-55-8512     TCGA-55-8513     TCGA-55-8514     TCGA-55-8614 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-8615     TCGA-55-8616     TCGA-55-8620     TCGA-55-A48Y 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A493     TCGA-55-A494 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-55-A4DG     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-64-1676     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-71-6725 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-71-8520     TCGA-73-4659     TCGA-73-4666     TCGA-73-4668 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-73-4670     TCGA-73-4675     TCGA-73-4676     TCGA-73-4677 
"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-78-7167 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-78-7220     TCGA-78-7535     TCGA-78-7536     TCGA-78-7537 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-78-7539     TCGA-78-7540     TCGA-78-7542     TCGA-78-8640 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-78-8648     TCGA-78-8655     TCGA-78-8662     TCGA-80-5608 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-83-5908     TCGA-86-6562     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-86-8358 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-8359     TCGA-86-8585     TCGA-86-8668     TCGA-86-8669 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-8671     TCGA-86-8672     TCGA-86-8673     TCGA-86-8674 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-86-A456     TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6828 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-91-6829     TCGA-91-6835     TCGA-91-6840     TCGA-91-A4BD 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-93-7347     TCGA-93-7348     TCGA-93-A4JN     TCGA-93-A4JO 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-93-A4JP     TCGA-95-7944     TCGA-95-8039     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-99-7458     TCGA-99-8025     TCGA-99-8028     TCGA-99-8032 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-99-8033     TCGA-J2-A4AD     TCGA-J2-A4AE     TCGA-J2-A4AG 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-L4-A4E5     TCGA-L4-A4E6     TCGA-MN-A4N4     TCGA-MN-A4N5 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-MP-A4SV     TCGA-MP-A4SW     TCGA-MP-A4SY     TCGA-MP-A4T2 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-MP-A4T4     TCGA-MP-A4T6     TCGA-MP-A4T7     TCGA-MP-A4T9 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-MP-A4TE     TCGA-MP-A4TF     TCGA-MP-A4TH     TCGA-MP-A4TI 
"MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" "MCM9 WILD-TYPE" 
    TCGA-MP-A4TK     TCGA-MP-A5C7     TCGA-NJ-A4YQ 
"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                        30   375
D68V14, multiclass
                                  clus
vv                                 MCM9 MUTATED MCM9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             30
  WHITE                                       3            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"
D68V15, binary
                cls
clus               0   1
  MCM9 MUTATED     0   3
  MCM9 WILD-TYPE   6 348
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      0    3
  MCM9 WILD-TYPE    6  348
                        clus
vv                       MCM9 MUTATED MCM9 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            3            348
[1] 2 2
[1] FALSE

Clustering(69) Variable = NCKAP1L MUTATION ANALYSIS
D69V1, survival
                   sevent
clus2                 0   1
  NCKAP1L MUTATED    10   9
  NCKAP1L WILD-TYPE 288 162
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
               19               450 
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
                9               162 
$`NCKAP1L MUTATED`
TCGA-05-4396 TCGA-44-7670 TCGA-55-1592 TCGA-73-4658 TCGA-78-7633 TCGA-95-A4VK 
        9.96        29.00        23.05        52.60        50.24        21.40 
TCGA-L9-A444 TCGA-05-4432 TCGA-44-7667 TCGA-50-5930 TCGA-50-5946 TCGA-55-7907 
       10.09        25.02        36.07         9.27        53.16        11.28 
TCGA-55-8092 TCGA-67-3771 TCGA-78-7162 TCGA-78-7536 TCGA-95-7039 TCGA-99-8028 
        5.06        20.05       104.19         8.02        41.82        36.76 
TCGA-MN-A4N4 
       38.63 

$`NCKAP1L WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       29.23         9.37        11.08        46.72        16.04        17.16 
TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1595 TCGA-55-6978 
       11.64        40.60        21.47        41.69        48.62         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.79         7.99        16.01        23.18        14.53        21.44 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 
        6.15        19.66        19.73        17.98        16.93        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 
       32.12        18.15        13.68        16.93        22.65        20.58 
TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4662 TCGA-73-7498 
       19.59        20.19        20.65        13.87        82.68        39.09 
TCGA-78-7166 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
        8.48        10.55        85.32        13.71        16.18         1.45 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
        6.12        17.29        16.54         2.86        15.68        15.65 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       18.18        17.92        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       24.30        23.80         6.35        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       29.98        12.00        30.02        21.99        26.01        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         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-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
        7.17        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       47.41        49.28         8.22        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 
       15.12        48.46        60.72        57.53        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05        12.16         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99        36.79        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       35.21        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       40.73        15.25        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
       70.26        31.30        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
       22.03         3.91        23.15        25.41        15.39        18.64 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       34.19        17.65        18.44        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       15.19        23.08        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       13.74        20.28        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.62        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        3.25         0.92        15.81        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-67-3772 
        2.04        42.90        28.41        51.25        28.47        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
       14.04        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
       13.41        13.51        14.01        13.45         4.24        19.43 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        8.42         6.90        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       30.31         9.24         1.25        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 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-78-7167 
        5.88        64.90        22.92         9.57       238.29        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       26.53        31.20        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
        1.08        19.00        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       15.39        16.41        14.30        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8032 
       19.76        20.84        18.67        24.56        34.85         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.57        18.08        35.47        32.48        19.00        14.30 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.85         5.49        41.59        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        47.08         0.49         0.43        19.82        59.11 

  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
             5.06              0.00 
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
           104.19            238.29 
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
            25.02             21.44 
[1] "5.1 - 104.2 (25.0)" "0.0 - 238.3 (21.4)"
[1] "hr=" "1.2"
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      114      130        44        62         67
                   vv
clus                STAGE IIIB STAGE IV
  NCKAP1L MUTATED            1        0
  NCKAP1L WILD-TYPE         10       24
D69V3, multiclass
            clus
vv           NCKAP1L MUTATED NCKAP1L WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 7               114
  STAGE IB                 2               130
  STAGE IIA                2                44
  STAGE IIB                4                62
  STAGE IIIA               3                67
  STAGE IIIB               1                10
  STAGE IV                 0                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
  NCKAP1L MUTATED     7   8   3   1
  NCKAP1L WILD-TYPE 149 253  40  17
D69V4, multiclass
    clus
vv   NCKAP1L MUTATED NCKAP1L WILD-TYPE
  T1               7               149
  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 296  85    69
D69V5, multiclass
       clus
vv      NCKAP1L MUTATED NCKAP1L WILD-TYPE
  N0                 12               296
  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 252 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NCKAP1L MUTATED      8   11
  NCKAP1L WILD-TYPE  252  210
        clus
vv       NCKAP1L MUTATED NCKAP1L WILD-TYPE
  FEMALE               8               252
  MALE                11               210
[1] 2 2
[1] FALSE
D69V8, binary
                   cls
clus                  0   1
  NCKAP1L MUTATED    13   3
  NCKAP1L WILD-TYPE 371  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NCKAP1L MUTATED     13    3
  NCKAP1L WILD-TYPE  371   52
     clus
vv    NCKAP1L MUTATED NCKAP1L WILD-TYPE
  NO               13               371
  YES               3                52
[1] 2 2
[1] FALSE
D69V9, continuous
[1] "Remove cluster labels:" "NCKAP1L MUTATED"       
clus
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
                1               121 
       TCGA-44-6147        TCGA-44-A47F        TCGA-49-6742        TCGA-55-7573 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-55-7725        TCGA-55-7914        TCGA-55-8205        TCGA-55-8511 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-55-8619        TCGA-55-8621        TCGA-55-A491        TCGA-55-A492 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-64-1677        TCGA-73-4662        TCGA-73-7498        TCGA-93-8067 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-MN-A4N1        TCGA-35-4122        TCGA-35-4123        TCGA-35-5375 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-44-3396        TCGA-44-3918        TCGA-44-4112        TCGA-44-6144 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-44-6775        TCGA-44-7660        TCGA-49-4486        TCGA-49-4494 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-49-4505        TCGA-49-4506        TCGA-49-4510        TCGA-49-6743 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-49-6744        TCGA-53-7624        TCGA-53-A4EZ        TCGA-55-5899 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-55-7283        TCGA-55-7574        TCGA-55-7910        TCGA-55-7913 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-55-7995        TCGA-55-8089        TCGA-55-8096        TCGA-55-8208 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-55-8507        TCGA-55-8508        TCGA-55-8512        TCGA-55-8513 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-55-8620        TCGA-55-A48Z        TCGA-55-A490        TCGA-55-A494 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-62-8394        TCGA-62-8395        TCGA-62-8397        TCGA-62-8398 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-62-8399        TCGA-62-8402        TCGA-62-A46O        TCGA-62-A46P 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-62-A46R        TCGA-62-A46S        TCGA-62-A46U        TCGA-62-A46V 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-62-A46Y        TCGA-62-A470        TCGA-62-A471        TCGA-62-A472 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-64-1681        TCGA-64-5775        TCGA-64-5778        TCGA-69-7974 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-69-8254        TCGA-71-6725        TCGA-71-8520        TCGA-73-4659 
"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-73-7499        TCGA-75-5122        TCGA-83-5908 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-86-6562        TCGA-86-6851        TCGA-86-7701        TCGA-86-7711 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-86-7713        TCGA-86-7714        TCGA-86-7953        TCGA-86-7954 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-86-7955        TCGA-86-8054        TCGA-86-8055        TCGA-86-8056 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-86-8073        TCGA-86-8074        TCGA-86-8075        TCGA-86-8076 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-86-8278        TCGA-86-8279        TCGA-86-8280        TCGA-86-8281 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-86-8358        TCGA-86-8359        TCGA-86-8668        TCGA-86-8669 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-86-8671        TCGA-86-A456        TCGA-86-A4JF        TCGA-86-A4P7 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-91-6829        TCGA-91-6849        TCGA-93-7347        TCGA-93-7348 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-93-A4JN        TCGA-93-A4JO        TCGA-95-7567        TCGA-99-7458 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-MN-A4N5 
"NCKAP1L WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  NCKAP1L MUTATED                            0
  NCKAP1L WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  NCKAP1L MUTATED                                   7
  NCKAP1L WILD-TYPE                                95
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  NCKAP1L MUTATED                                                   12
  NCKAP1L WILD-TYPE                                                284
                   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                                        17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 95
  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"
D69V11, continuous
D69V12, continuous
                   vv
clus                 R0  R1  R2  RX
  NCKAP1L MUTATED    13   0   0   1
  NCKAP1L WILD-TYPE 299  12   4  24
D69V13, multiclass
    clus
vv   NCKAP1L MUTATED NCKAP1L WILD-TYPE
  R0              13               299
  R1               0                12
  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                        28   363
D69V14, multiclass
                                  clus
vv                                 NCKAP1L MUTATED NCKAP1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      2                28
  WHITE                                         15               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"
D69V15, binary
                   cls
clus                  0   1
  NCKAP1L MUTATED     1  12
  NCKAP1L WILD-TYPE   5 339
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NCKAP1L MUTATED      1   12
  NCKAP1L WILD-TYPE    5  339
                        clus
vv                       NCKAP1L MUTATED NCKAP1L WILD-TYPE
  HISPANIC OR LATINO                   1                 5
  NOT HISPANIC OR LATINO              12               339
[1] 2 2
[1] FALSE

Clustering(70) Variable = ESYT3 MUTATION ANALYSIS
D70V1, survival
                 sevent
clus2               0   1
  ESYT3 MUTATED     4   4
  ESYT3 WILD-TYPE 294 167
  ESYT3 MUTATED ESYT3 WILD-TYPE 
              8             461 
  ESYT3 MUTATED ESYT3 WILD-TYPE 
              4             167 
$`ESYT3 MUTATED`
TCGA-38-7271 TCGA-44-7661 TCGA-05-4397 TCGA-05-5425 TCGA-55-8089 TCGA-55-8506 
       26.30        18.31        24.03        29.00        23.08         0.36 
TCGA-62-A46U TCGA-91-6849 
       67.96         1.15 

$`ESYT3 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7670 
       14.73        38.10        23.93        27.78        86.01        29.00 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       29.23         9.37        11.08        46.72        16.04        17.16 
TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 
       11.64        40.60        21.47        41.69        23.05        48.62 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        5.79         7.79         7.99        16.01        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       21.44         6.15        19.66        19.73        17.98        16.93 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       19.69        32.12        18.15        13.68        16.93        22.65 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       20.58        19.59        20.19        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       13.71        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        10.09        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       47.05        19.00         2.99        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
        4.96        22.03         9.04         2.04         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 
        8.68        97.74       120.79        37.71        49.05        44.61 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
        4.37        46.98        44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       23.77        19.56        23.15        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
       61.28        16.44        22.72        19.46         7.17        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       18.87        23.64        12.66         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
        9.44        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 
       29.46        29.75        55.89        53.29        55.33        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       49.28         8.22         9.27        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
        3.91        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99        36.79        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       13.94        35.21        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
      107.21        70.26        31.30        28.67        20.02        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
       32.71        22.03         3.91        23.15        25.41        15.39 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       18.64        11.28        34.19        17.65        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       29.23        29.72        15.19         5.06        17.79        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       15.65        29.19        22.16        15.42        17.56        15.72 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
       14.47        13.74        20.28        17.72        19.96        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
       17.10        17.62        14.66         1.58        12.33        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 
       21.40         3.25         0.92        15.81        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-64-1679 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-69-7760 
       18.84        14.04        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41        13.41        13.51        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       19.43         8.42         6.90        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 
        4.31        30.31         9.24         1.25        50.33        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       77.85        43.82        85.15        49.84        36.66       108.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
      100.57       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-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      238.29        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       26.01        39.35        10.55       232.18        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
      110.50        93.11        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 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 
       11.61        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-91-6840 TCGA-91-6847 
       41.36         1.97        10.19         2.60        12.23        27.68 
TCGA-91-6848 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        7.36        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 
       17.46        23.61         1.08        19.00        41.82        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       12.39        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       21.60        20.58        21.44        19.76        20.84        18.67 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
       24.56        34.85        36.76         1.45        21.57        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 
       35.47        32.48        19.00        14.30        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        5.49        41.59        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       47.08         0.49         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 
         23.555          21.440 
[1] "0.4 - 68.0 (23.6)"  "0.0 - 238.3 (21.4)"
[1] "hr=" "1.7"
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      119      131        46        62         69
                 vv
clus              STAGE IIIB STAGE IV
  ESYT3 MUTATED            0        0
  ESYT3 WILD-TYPE         11       24
D70V3, multiclass
            clus
vv           ESYT3 MUTATED ESYT3 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             119
  STAGE IB               1             131
  STAGE IIA              0              46
  STAGE IIB              4              62
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              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
  ESYT3 MUTATED     2   5   1   0
  ESYT3 WILD-TYPE 154 256  42  18
D70V4, multiclass
    clus
vv   ESYT3 MUTATED ESYT3 WILD-TYPE
  T1             2             154
  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 304  86    71
D70V5, multiclass
       clus
vv      ESYT3 MUTATED ESYT3 WILD-TYPE
  N0                4             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"
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 255 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT3 MUTATED      5    3
  ESYT3 WILD-TYPE  255  218
        clus
vv       ESYT3 MUTATED ESYT3 WILD-TYPE
  FEMALE             5             255
  MALE               3             218
[1] 2 2
[1] FALSE
D70V8, binary
                 cls
clus                0   1
  ESYT3 MUTATED     4   1
  ESYT3 WILD-TYPE 380  54
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT3 MUTATED      4    1
  ESYT3 WILD-TYPE  380   54
     clus
vv    ESYT3 MUTATED ESYT3 WILD-TYPE
  NO              4             380
  YES             1              54
[1] 2 2
[1] FALSE
D70V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ESYT3 MUTATED                            0                                 3
  ESYT3 WILD-TYPE                         17                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ESYT3 MUTATED                                                    5
  ESYT3 WILD-TYPE                                                291
                 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                                      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                               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 306  12   4  25
D70V13, multiclass
    clus
vv   ESYT3 MUTATED ESYT3 WILD-TYPE
  R0             6             306
  R1             0              12
  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                        29   373
D70V14, multiclass
                                  clus
vv                                 ESYT3 MUTATED ESYT3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              29
  WHITE                                        5             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"
D70V15, binary
                 cls
clus                0   1
  ESYT3 MUTATED     0   6
  ESYT3 WILD-TYPE   6 345
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT3 MUTATED      0    6
  ESYT3 WILD-TYPE    6  345
                        clus
vv                       ESYT3 MUTATED ESYT3 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             345
[1] 2 2
[1] FALSE

Clustering(71) Variable = MIA2 MUTATION ANALYSIS
D71V1, survival
                sevent
clus2              0   1
  MIA2 MUTATED     8   5
  MIA2 WILD-TYPE 290 166
  MIA2 MUTATED MIA2 WILD-TYPE 
            13            456 
  MIA2 MUTATED MIA2 WILD-TYPE 
             5            166 
$`MIA2 MUTATED`
TCGA-38-4629 TCGA-38-4630 TCGA-55-8203 TCGA-91-7771 TCGA-05-4424 TCGA-50-5944 
       28.41        35.28        17.98        16.18        30.02        57.53 
TCGA-55-5899 TCGA-55-A4DG TCGA-78-7152 TCGA-78-7155 TCGA-86-6851 TCGA-91-6831 
       30.58        19.99        39.95        38.50         5.88        10.19 
TCGA-MP-A4TK 
       19.13 

$`MIA2 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       26.01        15.02        15.02        11.64        14.73        26.30 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       38.10        23.93        27.78        86.01        18.31        29.00 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       29.23         9.37        11.08        46.72        16.04        17.16 
TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 
       11.64        40.60        21.47        41.69        23.05        48.62 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        5.79         7.79         7.99        16.01        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8204 TCGA-55-8205 
       21.44         6.15        19.66        19.73        16.93        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 
       32.12        18.15        13.68        16.93        22.65        20.58 
TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       19.59        20.19        20.65        13.87        52.60        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 
       39.09         8.48        50.24        10.55        85.32        13.71 
TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 
        1.45         6.12        17.29        16.54         2.86        15.68 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 
       15.65        21.40        18.18        17.92        20.19        20.52 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 
       17.75        20.68        24.30        23.80         6.35        10.09 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 
       27.19         5.29        31.23         2.43        10.09        50.07 
TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 
        3.98        45.01        37.02         0.00        24.03        47.05 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
       19.00         2.99        14.96        29.98        12.00        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       26.01        25.02        25.02        24.00         4.96        29.00 
TCGA-05-5428 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-38-4632 TCGA-38-A44F 
       97.74       120.79        37.71        49.05        44.61         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       46.98        44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       19.56        23.15        21.63        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        22.72        19.46         7.17        36.07        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         8.55        15.98        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 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-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 
       29.75        55.89        53.29        55.33        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47       101.72        15.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
        8.22         9.27        14.27        78.67         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       48.46        60.72        53.16        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05        12.16         6.21         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.79        27.25        34.29        30.54        13.94        35.21 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       14.30        80.52         5.62        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       46.03        53.65         3.88        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       92.81        24.99        40.54       107.21        70.26        31.30 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
       28.67        20.02        27.09        32.71        22.03         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
       23.15        25.41        15.39        18.64        11.28        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       23.08         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       13.74        20.28        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.62        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        3.25         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-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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       29.92        56.81        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-69-7760 TCGA-69-7761 
       14.04        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
       13.41        13.51        14.01        13.45         4.24        19.43 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        8.42         6.90        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       30.31         9.24         1.25        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       21.90       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-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-7701 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        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6840 
       26.47        10.62        41.36         1.97         2.60        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45        17.46        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       41.82        18.67        12.39        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       42.25        64.60        63.52        61.48        25.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59        15.91        18.67         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.57        18.08        35.47        32.48        19.00        14.30 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       24.36        14.10        73.91        71.05        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        47.08         0.49         0.43        19.82        59.11 

  MIA2 MUTATED MIA2 WILD-TYPE 
          5.88           0.00 
  MIA2 MUTATED MIA2 WILD-TYPE 
         57.53         238.29 
  MIA2 MUTATED MIA2 WILD-TYPE 
        28.410         21.455 
[1] "5.9 - 57.5 (28.4)"  "0.0 - 238.3 (21.5)"
[1] "hr=" "1.1"
D71V2, continuous
                vv
clus             STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  MIA2 MUTATED         0        3        4         1         4          0
  MIA2 WILD-TYPE       4      118      128        45        62         70
                vv
clus             STAGE IIIB STAGE IV
  MIA2 MUTATED            0        0
  MIA2 WILD-TYPE         11       24
D71V3, multiclass
            clus
vv           MIA2 MUTATED MIA2 WILD-TYPE
  STAGE I               0              4
  STAGE IA              3            118
  STAGE IB              4            128
  STAGE IIA             1             45
  STAGE IIB             4             62
  STAGE IIIA            0             70
  STAGE IIIB            0             11
  STAGE IV              0             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
  MIA2 MUTATED     5   5   3   0
  MIA2 WILD-TYPE 151 256  40  18
D71V4, multiclass
    clus
vv   MIA2 MUTATED MIA2 WILD-TYPE
  T1            5            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
  MIA2 MUTATED    10   3     0
  MIA2 WILD-TYPE 298  86    72
D71V5, multiclass
       clus
vv      MIA2 MUTATED MIA2 WILD-TYPE
  N0              10            298
  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 255 213
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA2 MUTATED      5    8
  MIA2 WILD-TYPE  255  213
        clus
vv       MIA2 MUTATED MIA2 WILD-TYPE
  FEMALE            5            255
  MALE              8            213
[1] 2 2
[1] FALSE
D71V8, binary
                cls
clus               0   1
  MIA2 MUTATED    11   1
  MIA2 WILD-TYPE 373  54
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA2 MUTATED     11    1
  MIA2 WILD-TYPE  373   54
     clus
vv    MIA2 MUTATED MIA2 WILD-TYPE
  NO            11            373
  YES            1             54
[1] 2 2
[1] FALSE
D71V9, continuous
[1] "Remove cluster labels:" "MIA2 MUTATED"          
clus
  MIA2 MUTATED MIA2 WILD-TYPE 
             2            120 
    TCGA-44-6147     TCGA-44-A47F     TCGA-49-6742     TCGA-55-7573 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-55-7725     TCGA-55-7914     TCGA-55-8205     TCGA-55-8511 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-55-8619     TCGA-55-8621     TCGA-55-A491     TCGA-55-A492 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-64-1677     TCGA-73-4662     TCGA-73-7498     TCGA-93-8067 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-MN-A4N1     TCGA-35-4122     TCGA-35-4123     TCGA-35-5375 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-44-3396     TCGA-44-3918     TCGA-44-4112     TCGA-44-6144 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-44-6775     TCGA-44-7660     TCGA-49-4486     TCGA-49-4494 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-49-4505     TCGA-49-4506     TCGA-49-4510     TCGA-49-6743 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-49-6744     TCGA-53-7624     TCGA-53-A4EZ     TCGA-55-7283 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-55-7574     TCGA-55-7910     TCGA-55-7913     TCGA-55-7995 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-55-8089     TCGA-55-8096     TCGA-55-8208     TCGA-55-8507 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-55-8508     TCGA-55-8512     TCGA-55-8513     TCGA-55-8620 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-55-A48Z     TCGA-55-A490     TCGA-55-A494     TCGA-62-8394 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-62-8395     TCGA-62-8397     TCGA-62-8398     TCGA-62-8399 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-62-8402     TCGA-62-A46O     TCGA-62-A46P     TCGA-62-A46R 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-62-A46S     TCGA-62-A46U     TCGA-62-A46V     TCGA-62-A46Y 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-62-A470     TCGA-62-A471     TCGA-62-A472     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-73-4666 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-73-4668     TCGA-73-4670     TCGA-73-4676     TCGA-73-4677 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-73-7499     TCGA-75-5122     TCGA-83-5908     TCGA-86-6562 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-86-7701     TCGA-86-7711     TCGA-86-7713     TCGA-86-7714 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-86-7953     TCGA-86-7954     TCGA-86-7955     TCGA-86-8054 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-86-8055     TCGA-86-8056     TCGA-86-8073     TCGA-86-8074 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-86-8075     TCGA-86-8076     TCGA-86-8278     TCGA-86-8279 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-86-8280     TCGA-86-8281     TCGA-86-8358     TCGA-86-8359 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-86-8668     TCGA-86-8669     TCGA-86-8671     TCGA-86-A456 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-86-A4JF     TCGA-86-A4P7     TCGA-91-6829     TCGA-91-6849 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-93-7347     TCGA-93-7348     TCGA-93-A4JN     TCGA-93-A4JO 
"MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" "MIA2 WILD-TYPE" 
    TCGA-95-7567     TCGA-99-7458     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                         16                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  MIA2 MUTATED                                                    8
  MIA2 WILD-TYPE                                                288
                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                                     16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  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"
D71V11, continuous
D71V12, continuous
                vv
clus              R0  R1  R2  RX
  MIA2 MUTATED     8   2   0   0
  MIA2 WILD-TYPE 304  10   4  25
D71V13, multiclass
    clus
vv   MIA2 MUTATED MIA2 WILD-TYPE
  R0            8            304
  R1            2             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
  MIA2 MUTATED                                  0     0
  MIA2 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MIA2 MUTATED                           0    11
  MIA2 WILD-TYPE                        30   367
D71V14, multiclass
                                  clus
vv                                 MIA2 MUTATED MIA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             30
  WHITE                                      11            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"
D71V15, binary
                cls
clus               0   1
  MIA2 MUTATED     0   8
  MIA2 WILD-TYPE   6 343
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA2 MUTATED      0    8
  MIA2 WILD-TYPE    6  343
                        clus
vv                       MIA2 MUTATED MIA2 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            8            343
[1] 2 2
[1] FALSE

Clustering(72) Variable = TUBB4 MUTATION ANALYSIS
D72V1, survival
                 sevent
clus2               0   1
  TUBB4 MUTATED    13   4
  TUBB4 WILD-TYPE 285 167
  TUBB4 MUTATED TUBB4 WILD-TYPE 
             17             452 
  TUBB4 MUTATED TUBB4 WILD-TYPE 
              4             167 
$`TUBB4 MUTATED`
TCGA-44-8119 TCGA-73-4662 TCGA-91-A4BC TCGA-L9-A444 TCGA-05-4397 TCGA-53-7813 
        9.37        82.68         1.45        10.09        24.03        13.94 
TCGA-55-6985 TCGA-55-7576 TCGA-55-A490 TCGA-64-5778 TCGA-64-5781 TCGA-67-4679 
       40.54        22.03         3.25        42.90        51.25        14.73 
TCGA-69-7980 TCGA-75-6214 TCGA-97-8174 TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       13.51        36.66         5.39         1.64        47.08 

$`TUBB4 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       18.31        29.00        29.23        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       52.60        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       13.71        16.18         6.12        17.29        16.54         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       15.68        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 
       27.19         5.29        31.23         2.43        10.09        50.07 
TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4403 
        3.98        45.01        37.02         0.00        47.05        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       26.01        25.02        25.02        24.00         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 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-38-4632 TCGA-38-A44F 
       97.74       120.79        37.71        49.05        44.61         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       46.98        44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       19.56        23.15        21.63        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        22.72        19.46         7.17        36.07        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         8.55        15.98        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 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-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 
       29.75        55.89        53.29        55.33        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47       101.72        15.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
        8.22         9.27        14.27        78.67         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       48.46        60.72        57.53        53.16        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05        12.16         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ 
       36.99        36.79        27.25        34.29        30.54        35.21 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       30.58        14.30        80.52         5.62        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       15.25        46.03        53.65         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       32.71        92.81        24.99       107.21        70.26        31.30 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7727 TCGA-55-7728 
       28.67        20.02        27.09        32.71         3.91        23.15 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       25.41        15.39        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.44        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42        17.56        15.72        14.47         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A493 
       14.66         1.58        12.33        20.71        21.40         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 
       56.81        81.80        38.37        87.98         2.04        28.41 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
       28.47        20.05        18.84        14.04         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         4.41        13.41        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       19.43         8.42         6.90        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 
        4.31        30.31         9.24         1.25        50.33        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 
       77.85        43.82        85.15        49.84       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 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        11.61 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-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-91-6840 TCGA-91-6847 TCGA-91-6848 
        1.97        10.19         2.60        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 
       17.46        23.61         1.08        19.00        41.82        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       12.39        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
       18.67        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       20.58        21.44        19.76        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE 
       34.85        36.76         1.45        21.57        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       32.48        19.00        14.30        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       41.59        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A55A TCGA-NJ-A55O 
       73.91        71.05        74.33         0.13         0.49         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  TUBB4 MUTATED TUBB4 WILD-TYPE 
           1.45            0.00 
  TUBB4 MUTATED TUBB4 WILD-TYPE 
          82.68          238.29 
  TUBB4 MUTATED TUBB4 WILD-TYPE 
          14.73           21.47 
[1] "1.4 - 82.7 (14.7)"  "0.0 - 238.3 (21.5)"
[1] "hr=" "1.4"
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      118      127        43        64         69
                 vv
clus              STAGE IIIB STAGE IV
  TUBB4 MUTATED            1        0
  TUBB4 WILD-TYPE         10       24
D72V3, multiclass
            clus
vv           TUBB4 MUTATED TUBB4 WILD-TYPE
  STAGE I                1               3
  STAGE IA               3             118
  STAGE IB               5             127
  STAGE IIA              3              43
  STAGE IIB              2              64
  STAGE IIIA             1              69
  STAGE IIIB             1              10
  STAGE IV               0              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
  TUBB4 MUTATED     4  10   2   1
  TUBB4 WILD-TYPE 152 251  41  17
D72V4, multiclass
    clus
vv   TUBB4 MUTATED TUBB4 WILD-TYPE
  T1             4             152
  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 293  88    71
D72V5, multiclass
       clus
vv      TUBB4 MUTATED TUBB4 WILD-TYPE
  N0               15             293
  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 252 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBB4 MUTATED      8    9
  TUBB4 WILD-TYPE  252  212
        clus
vv       TUBB4 MUTATED TUBB4 WILD-TYPE
  FEMALE             8             252
  MALE               9             212
[1] 2 2
[1] FALSE
D72V8, binary
                 cls
clus                0   1
  TUBB4 MUTATED    14   0
  TUBB4 WILD-TYPE 370  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBB4 MUTATED     14    0
  TUBB4 WILD-TYPE  370   55
     clus
vv    TUBB4 MUTATED TUBB4 WILD-TYPE
  NO             14             370
  YES             0              55
[1] 2 2
[1] FALSE
D72V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TUBB4 MUTATED                            0                                 2
  TUBB4 WILD-TYPE                         17                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TUBB4 MUTATED                                                   11
  TUBB4 WILD-TYPE                                                285
                 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                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             285
  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 302  12   4  24
D72V13, multiclass
    clus
vv   TUBB4 MUTATED TUBB4 WILD-TYPE
  R0            10             302
  R1             0              12
  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                        29   364
D72V14, multiclass
                                  clus
vv                                 TUBB4 MUTATED TUBB4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              29
  WHITE                                       14             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"
D72V15, binary
                 cls
clus                0   1
  TUBB4 MUTATED     0  14
  TUBB4 WILD-TYPE   6 337
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBB4 MUTATED      0   14
  TUBB4 WILD-TYPE    6  337
                        clus
vv                       TUBB4 MUTATED TUBB4 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            14             337
[1] 2 2
[1] FALSE

Clustering(73) Variable = ABHD12B MUTATION ANALYSIS
D73V1, survival
                   sevent
clus2                 0   1
  ABHD12B MUTATED     3   4
  ABHD12B WILD-TYPE 295 167
  ABHD12B MUTATED ABHD12B WILD-TYPE 
                7               462 
  ABHD12B MUTATED ABHD12B WILD-TYPE 
                4               167 
$`ABHD12B MUTATED`
TCGA-49-4501 TCGA-44-6779 TCGA-55-6968 TCGA-55-7994 TCGA-78-7147 TCGA-99-8032 
       46.72        16.44        42.51        19.82        19.27         1.45 
TCGA-NJ-A4YP 
        1.64 

$`ABHD12B WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-6742 
       18.31        29.00        29.23         9.37        11.08        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       29.98        12.00        30.02        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       25.02        24.00         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       37.71        49.05        44.61         4.37        46.98        44.42 
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-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 
       21.63        23.18        32.45        61.28        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       55.33        22.26        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       53.16        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 
       34.29        30.54        13.94        35.21        30.58        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
       80.52         5.62        40.73        15.25        46.03        53.65 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26        31.30        28.67        20.02 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       27.09        32.71        22.03         3.91        23.15        25.41 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 
       15.39        18.64        11.28        34.19        17.65        18.44 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       29.23        29.72        15.19        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.72        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       19.96        26.01        17.10        17.62        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       12.33        20.71        21.40         3.25         0.92        15.81 
TCGA-55-A4DG TCGA-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-64-1679 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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        19.43         8.42         6.90 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       23.38        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
        1.25        50.33        66.64        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       49.84        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        5.69        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        9.57       104.19       238.29        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59       110.50        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.18        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
       19.00        41.82        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       15.39        16.41        14.30        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       19.76        20.84        18.67        24.56        34.85        36.76 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.57        18.08        35.47        32.48        19.00        14.30 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.13        47.08         0.49         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             21.52 
[1] "1.4 - 46.7 (19.3)"  "0.0 - 238.3 (21.5)"
[1] "hr=" "2.1"
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      120      130        46        63         70
                   vv
clus                STAGE IIIB STAGE IV
  ABHD12B MUTATED            0        1
  ABHD12B WILD-TYPE         11       23
D73V3, multiclass
            clus
vv           ABHD12B MUTATED ABHD12B WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 1               120
  STAGE IB                 2               130
  STAGE IIA                0                46
  STAGE IIB                3                63
  STAGE IIIA               0                70
  STAGE IIIB               0                11
  STAGE IV                 1                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
  ABHD12B MUTATED     2   4   1   0
  ABHD12B WILD-TYPE 154 257  42  18
D73V4, multiclass
    clus
vv   ABHD12B MUTATED ABHD12B WILD-TYPE
  T1               2               154
  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 303  87    72
D73V5, multiclass
       clus
vv      ABHD12B MUTATED ABHD12B WILD-TYPE
  N0                  5               303
  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 257 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ABHD12B MUTATED      3    4
  ABHD12B WILD-TYPE  257  217
        clus
vv       ABHD12B MUTATED ABHD12B WILD-TYPE
  FEMALE               3               257
  MALE                 4               217
[1] 2 2
[1] FALSE
D73V8, binary
                   cls
clus                  0   1
  ABHD12B MUTATED     6   1
  ABHD12B WILD-TYPE 378  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ABHD12B MUTATED      6    1
  ABHD12B WILD-TYPE  378   54
     clus
vv    ABHD12B MUTATED ABHD12B WILD-TYPE
  NO                6               378
  YES               1                54
[1] 2 2
[1] FALSE
D73V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  ABHD12B MUTATED                            0
  ABHD12B WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  ABHD12B MUTATED                                   0
  ABHD12B WILD-TYPE                               102
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ABHD12B MUTATED                                                    6
  ABHD12B WILD-TYPE                                                290
                   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                                        17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                102
  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"
D73V11, continuous
D73V12, continuous
                   vv
clus                 R0  R1  R2  RX
  ABHD12B MUTATED     4   0   0   0
  ABHD12B WILD-TYPE 308  12   4  25
D73V13, multiclass
    clus
vv   ABHD12B MUTATED ABHD12B WILD-TYPE
  R0               4               308
  R1               0                12
  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                        30   371
D73V14, multiclass
                                  clus
vv                                 ABHD12B MUTATED ABHD12B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                30
  WHITE                                          7               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"
D73V15, binary
                   cls
clus                  0   1
  ABHD12B MUTATED     0   5
  ABHD12B WILD-TYPE   6 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ABHD12B MUTATED      0    5
  ABHD12B WILD-TYPE    6  346
                        clus
vv                       ABHD12B MUTATED ABHD12B WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               5               346
[1] 2 2
[1] FALSE

Clustering(74) Variable = ANTXR1 MUTATION ANALYSIS
D74V1, survival
                  sevent
clus2                0   1
  ANTXR1 MUTATED    12   7
  ANTXR1 WILD-TYPE 286 164
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
              19              450 
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
               7              164 
$`ANTXR1 MUTATED`
TCGA-55-A491 TCGA-L9-A443 TCGA-L9-A444 TCGA-38-4626 TCGA-49-4487 TCGA-55-7574 
       20.58         6.35        10.09       120.79        28.11        32.71 
TCGA-55-7903 TCGA-55-7907 TCGA-55-8092 TCGA-62-A472 TCGA-64-5779 TCGA-67-4679 
       18.64        11.28         5.06        29.92        28.41        14.73 
TCGA-67-6215 TCGA-73-4668 TCGA-78-8662 TCGA-97-7941 TCGA-97-8174 TCGA-99-8028 
        5.72        15.35       110.50        15.91         5.39        36.76 
TCGA-L4-A4E5 
       19.00 

$`ANTXR1 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       16.93        22.65        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       23.80        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       47.05        19.00         2.99        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-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-38-4627 TCGA-38-4628 TCGA-38-4632 
        5.98         8.68        97.74        37.71        49.05        44.61 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
        4.37        46.98        44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       23.77        19.56        23.15        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
       61.28        16.44        22.72        19.46         7.17        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       18.87        23.64        12.66         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 
        9.44        11.54        13.64        13.45        76.21        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 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-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 
       29.75        55.89        53.29        55.33        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47       101.72        15.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
        8.22         9.27        14.27        78.67         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       48.46        60.72        57.53        53.16        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05        12.16         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99        36.79        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       35.21        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       40.73        15.25        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7576 
       70.26        31.30        28.67        20.02        27.09        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7910 TCGA-55-7911 
        3.91        23.15        25.41        15.39        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.44        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       17.79        23.64        15.65        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       17.56        15.72        14.47         0.36        13.74        20.28 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
        1.58        12.33        20.71        21.40         3.25         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        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-64-1676 
       67.96        72.30        13.61        39.25        40.96        56.81 
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-67-6216 TCGA-69-7760 
       28.47        20.05        18.84        14.04         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41        13.41        13.51        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 
       19.43         8.42         6.90        23.38        26.30         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       30.31         9.24         1.25        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7167 TCGA-78-7220 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-80-5608 
       39.35        10.55       232.18        39.75        77.59        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       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        11.61        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        12.23        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
       23.61         1.08        19.00        41.82        18.67        12.39 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       27.29         2.76        19.89        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-8171 TCGA-97-8175 
       61.48        25.48        18.54         0.59        18.67        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       15.39        16.41        14.30        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8032 
       19.76        20.84        18.67        24.56        34.85         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-MN-A4N4 
       21.57        18.08        35.47        32.48        14.30        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.85         5.49        41.59        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        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        47.08         0.49         0.43        19.82        59.11 

  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
            5.06             0.00 
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
          120.79           238.29 
  ANTXR1 MUTATED ANTXR1 WILD-TYPE 
          18.640           21.585 
[1] "5.1 - 120.8 (18.6)" "0.0 - 238.3 (21.6)"
[1] "hr=" "1.1"
D74V2, continuous
                  vv
clus               STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  ANTXR1 MUTATED         1        7        3         2         3          1
  ANTXR1 WILD-TYPE       3      114      129        44        63         69
                  vv
clus               STAGE IIIB STAGE IV
  ANTXR1 MUTATED            0        0
  ANTXR1 WILD-TYPE         11       24
D74V3, multiclass
            clus
vv           ANTXR1 MUTATED ANTXR1 WILD-TYPE
  STAGE I                 1                3
  STAGE IA                7              114
  STAGE IB                3              129
  STAGE IIA               2               44
  STAGE IIB               3               63
  STAGE IIIA              1               69
  STAGE IIIB              0               11
  STAGE IV                0               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
  ANTXR1 MUTATED     8   8   3   0
  ANTXR1 WILD-TYPE 148 253  40  18
D74V4, multiclass
    clus
vv   ANTXR1 MUTATED ANTXR1 WILD-TYPE
  T1              8              148
  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 292  87    71
D74V5, multiclass
       clus
vv      ANTXR1 MUTATED ANTXR1 WILD-TYPE
  N0                16              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"
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 248 214
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANTXR1 MUTATED     12    7
  ANTXR1 WILD-TYPE  248  214
        clus
vv       ANTXR1 MUTATED ANTXR1 WILD-TYPE
  FEMALE             12              248
  MALE                7              214
[1] 2 2
[1] FALSE
D74V8, binary
                  cls
clus                 0   1
  ANTXR1 MUTATED    15   3
  ANTXR1 WILD-TYPE 369  52
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANTXR1 MUTATED     15    3
  ANTXR1 WILD-TYPE  369   52
     clus
vv    ANTXR1 MUTATED ANTXR1 WILD-TYPE
  NO              15              369
  YES              3               52
[1] 2 2
[1] FALSE
D74V9, continuous
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ANTXR1 MUTATED                            2                                 0
  ANTXR1 WILD-TYPE                         15                               102
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ANTXR1 MUTATED                                                   15
  ANTXR1 WILD-TYPE                                                281
                  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                                       15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               102
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              281
  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 295  11   4  25
D74V13, multiclass
    clus
vv   ANTXR1 MUTATED ANTXR1 WILD-TYPE
  R0             17              295
  R1              1               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
  ANTXR1 MUTATED                                  1     0
  ANTXR1 WILD-TYPE                                0     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ANTXR1 MUTATED                           1    16
  ANTXR1 WILD-TYPE                        29   362
D74V14, multiclass
                                  clus
vv                                 ANTXR1 MUTATED ANTXR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               29
  WHITE                                        16              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"
D74V15, binary
                  cls
clus                 0   1
  ANTXR1 MUTATED     0  18
  ANTXR1 WILD-TYPE   6 333
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANTXR1 MUTATED      0   18
  ANTXR1 WILD-TYPE    6  333
                        clus
vv                       ANTXR1 MUTATED ANTXR1 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO             18              333
[1] 2 2
[1] FALSE

Clustering(75) Variable = FLCN MUTATION ANALYSIS
D75V1, survival
                sevent
clus2              0   1
  FLCN MUTATED     4   5
  FLCN WILD-TYPE 294 166
  FLCN MUTATED FLCN WILD-TYPE 
             9            460 
  FLCN MUTATED FLCN WILD-TYPE 
             5            166 
$`FLCN MUTATED`
TCGA-55-8511 TCGA-05-4397 TCGA-53-7626 TCGA-55-7281 TCGA-62-A46O TCGA-78-7154 
       18.15        24.03        30.54        28.67        47.80        19.50 
TCGA-78-7537 TCGA-93-A4JN TCGA-97-8175 
       53.33        23.61        18.12 

$`FLCN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 
       17.98        16.93        19.69        32.12        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
        0.00        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         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-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       55.33        22.26        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       53.16        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       34.29        13.94        35.21        30.58        14.30        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        5.62        42.51        40.73        15.25        46.03        53.65 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7283 TCGA-55-7570 
       40.54       107.21        70.26        31.30        20.02        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
       32.71        22.03         3.91        23.15        25.41        15.39 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       18.64        11.28        34.19        17.65        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       29.23        29.72        15.19        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.72        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       19.96        26.01        17.10        17.62        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       12.33        20.71        21.40         3.25         0.92        15.81 
TCGA-55-A4DG TCGA-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-64-1679 
       13.61        39.25        40.96        29.92        56.81        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41        13.41        13.51        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 
       13.45         4.24        19.43         8.42         6.90        23.38 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
       50.33        66.64        77.85        43.82        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       36.66       108.66       100.57       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      104.19       238.29        88.14        26.53        31.20         8.02 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       26.01        39.35        10.55       232.18        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
      110.50        93.11        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 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 
       11.61        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-91-6840 TCGA-91-6847 
       41.36         1.97        10.19         2.60        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
        7.36         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 
       22.45        17.46         1.08        19.00        41.82        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       12.39        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
       18.67         5.39        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       20.58        21.44        19.76        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE 
       34.85        36.76         1.45        21.57        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       32.48        19.00        14.30        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       41.59        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.49         0.43        19.82        59.11 

  FLCN MUTATED FLCN WILD-TYPE 
         18.12           0.00 
  FLCN MUTATED FLCN WILD-TYPE 
         53.33         238.29 
  FLCN MUTATED FLCN WILD-TYPE 
         24.03          21.44 
[1] "18.1 - 53.3 (24.0)" "0.0 - 238.3 (21.4)"
[1] "hr=" "1.5"
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      120      128        45        65         69
                vv
clus             STAGE IIIB STAGE IV
  FLCN MUTATED            0        1
  FLCN WILD-TYPE         11       23
D75V3, multiclass
            clus
vv           FLCN MUTATED FLCN WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            120
  STAGE IB              4            128
  STAGE IIA             1             45
  STAGE IIB             1             65
  STAGE IIIA            1             69
  STAGE IIIB            0             11
  STAGE IV              1             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
  FLCN MUTATED     2   6   1   0
  FLCN WILD-TYPE 154 255  42  18
D75V4, multiclass
    clus
vv   FLCN MUTATED FLCN WILD-TYPE
  T1            2            154
  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 302  87    71
D75V5, multiclass
       clus
vv      FLCN MUTATED FLCN WILD-TYPE
  N0               6            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"
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 255 217
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLCN MUTATED      5    4
  FLCN WILD-TYPE  255  217
        clus
vv       FLCN MUTATED FLCN WILD-TYPE
  FEMALE            5            255
  MALE              4            217
[1] 2 2
[1] FALSE
D75V8, binary
                cls
clus               0   1
  FLCN MUTATED     7   0
  FLCN WILD-TYPE 377  55
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLCN MUTATED      7    0
  FLCN WILD-TYPE  377   55
     clus
vv    FLCN MUTATED FLCN WILD-TYPE
  NO             7            377
  YES            0             55
[1] 2 2
[1] FALSE
D75V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  FLCN MUTATED                            1                                 2
  FLCN WILD-TYPE                         16                               100
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  FLCN MUTATED                                                    5
  FLCN WILD-TYPE                                                291
                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                                     16
  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                   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 305  12   4  24
D75V13, multiclass
    clus
vv   FLCN MUTATED FLCN WILD-TYPE
  R0            7            305
  R1            0             12
  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                        30   371
D75V14, multiclass
                                  clus
vv                                 FLCN MUTATED FLCN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   0             30
  WHITE                                       7            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"
D75V15, binary
                cls
clus               0   1
  FLCN MUTATED     0   5
  FLCN WILD-TYPE   6 346
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLCN MUTATED      0    5
  FLCN WILD-TYPE    6  346
                        clus
vv                       FLCN MUTATED FLCN WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            5            346
[1] 2 2
[1] FALSE

Clustering(76) Variable = ZNF556 MUTATION ANALYSIS
D76V1, survival
                  sevent
clus2                0   1
  ZNF556 MUTATED     8   4
  ZNF556 WILD-TYPE 290 167
  ZNF556 MUTATED ZNF556 WILD-TYPE 
              12              457 
  ZNF556 MUTATED ZNF556 WILD-TYPE 
               4              167 
$`ZNF556 MUTATED`
TCGA-05-4405 TCGA-38-4630 TCGA-05-4424 TCGA-50-5946 TCGA-55-6982 TCGA-55-7994 
       20.05        35.28        30.02        53.16        32.71        19.82 
TCGA-55-8301 TCGA-69-7979 TCGA-91-6829 TCGA-97-8179 TCGA-99-8028 TCGA-MP-A4TF 
       17.56        13.41        41.36        14.30        36.76        11.05 

$`ZNF556 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96         8.02         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       15.02        15.02        28.41        11.64        14.73        26.30 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       38.10        23.93        27.78        86.01        18.31        29.00 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       29.23         9.37        11.08        46.72        16.04        17.16 
TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 
       11.64        40.60        21.47        41.69        23.05        48.62 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        5.79         7.79         7.99        16.01        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       21.44         6.15        19.66        19.73        17.98        16.93 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       19.69        32.12        18.15        13.68        16.93        22.65 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       20.58        19.59        20.19        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       13.71        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        10.09        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       12.00        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        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-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 
       44.61         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-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 
        8.45        15.12        48.46        60.72        57.53        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
        3.91        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99        36.79        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       13.94        35.21        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       69.34        45.34        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
       70.26        31.30        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
       22.03         3.91        23.15        25.41        15.39        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 
       11.28        34.19        17.65        18.44        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       15.19        23.08         5.06        17.79        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       29.19        22.16        15.42        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       13.74        20.28        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.62        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        3.25         0.92        15.81        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-69-7760 
       18.84        14.04        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 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-69-A59K 
        4.41        13.51        14.01        13.45         4.24        19.43 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        8.42         6.90        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       30.31         9.24         1.25        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 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        11.61 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-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-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
       23.61         1.08        19.00        41.82        18.67        12.39 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       27.29         2.76        19.89        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       61.48        25.48        18.54         0.59        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 
        5.39        18.12        15.39        16.41        21.60        20.58 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        1.45        21.57        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       14.30        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE 
       37.35        86.04        58.85         5.49        41.59        29.46 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        47.08         0.49         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  ZNF556 MUTATED ZNF556 WILD-TYPE 
           11.05             0.00 
  ZNF556 MUTATED ZNF556 WILD-TYPE 
           53.16           238.29 
  ZNF556 MUTATED ZNF556 WILD-TYPE 
          25.035           21.470 
[1] "11.1 - 53.2 (25.0)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1"  
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      118      127        45        63         70
                  vv
clus               STAGE IIIB STAGE IV
  ZNF556 MUTATED            0        0
  ZNF556 WILD-TYPE         11       24
D76V3, multiclass
            clus
vv           ZNF556 MUTATED ZNF556 WILD-TYPE
  STAGE I                 0                4
  STAGE IA                3              118
  STAGE IB                5              127
  STAGE IIA               1               45
  STAGE IIB               3               63
  STAGE IIIA              0               70
  STAGE IIIB              0               11
  STAGE IV                0               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
  ZNF556 MUTATED     3   7   2   0
  ZNF556 WILD-TYPE 153 254  41  18
D76V4, multiclass
    clus
vv   ZNF556 MUTATED ZNF556 WILD-TYPE
  T1              3              153
  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 297  88    72
D76V5, multiclass
       clus
vv      ZNF556 MUTATED ZNF556 WILD-TYPE
  N0                11              297
  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 254 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF556 MUTATED      6    6
  ZNF556 WILD-TYPE  254  215
        clus
vv       ZNF556 MUTATED ZNF556 WILD-TYPE
  FEMALE              6              254
  MALE                6              215
[1] 2 2
[1] FALSE
D76V8, binary
                  cls
clus                 0   1
  ZNF556 MUTATED    11   1
  ZNF556 WILD-TYPE 373  54
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF556 MUTATED     11    1
  ZNF556 WILD-TYPE  373   54
     clus
vv    ZNF556 MUTATED ZNF556 WILD-TYPE
  NO              11              373
  YES              1               54
[1] 2 2
[1] FALSE
D76V9, continuous
[1] "Remove cluster labels:" "ZNF556 MUTATED"        
clus
  ZNF556 MUTATED ZNF556 WILD-TYPE 
               1              121 
      TCGA-44-6147       TCGA-44-A47F       TCGA-49-6742       TCGA-55-7573 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-55-7725       TCGA-55-7914       TCGA-55-8205       TCGA-55-8511 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-55-8619       TCGA-55-8621       TCGA-55-A491       TCGA-55-A492 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-64-1677       TCGA-73-4662       TCGA-73-7498       TCGA-93-8067 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-MN-A4N1       TCGA-35-4122       TCGA-35-4123       TCGA-35-5375 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-44-3396       TCGA-44-3918       TCGA-44-4112       TCGA-44-6144 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-44-6775       TCGA-44-7660       TCGA-49-4486       TCGA-49-4494 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-49-4505       TCGA-49-4506       TCGA-49-4510       TCGA-49-6743 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-49-6744       TCGA-53-7624       TCGA-53-A4EZ       TCGA-55-5899 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-55-7283       TCGA-55-7574       TCGA-55-7910       TCGA-55-7913 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-55-7995       TCGA-55-8089       TCGA-55-8096       TCGA-55-8208 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-55-8507       TCGA-55-8508       TCGA-55-8512       TCGA-55-8513 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-55-8620       TCGA-55-A48Z       TCGA-55-A490       TCGA-55-A494 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-62-8394       TCGA-62-8395       TCGA-62-8397       TCGA-62-8398 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-62-8399       TCGA-62-8402       TCGA-62-A46O       TCGA-62-A46P 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-62-A46R       TCGA-62-A46S       TCGA-62-A46U       TCGA-62-A46V 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-62-A46Y       TCGA-62-A470       TCGA-62-A471       TCGA-62-A472 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-64-1681       TCGA-64-5775       TCGA-64-5778       TCGA-69-7974 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-69-8254       TCGA-71-6725       TCGA-71-8520       TCGA-73-4659 
"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-73-7499       TCGA-75-5122       TCGA-83-5908 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-86-6562       TCGA-86-6851       TCGA-86-7701       TCGA-86-7711 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-86-7713       TCGA-86-7714       TCGA-86-7953       TCGA-86-7954 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-86-7955       TCGA-86-8054       TCGA-86-8055       TCGA-86-8056 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-86-8073       TCGA-86-8074       TCGA-86-8075       TCGA-86-8076 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-86-8278       TCGA-86-8279       TCGA-86-8280       TCGA-86-8281 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-86-8358       TCGA-86-8359       TCGA-86-8668       TCGA-86-8669 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-86-8671       TCGA-86-A456       TCGA-86-A4JF       TCGA-86-A4P7 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-91-6849       TCGA-93-7347       TCGA-93-7348       TCGA-93-A4JN 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-93-A4JO       TCGA-95-7567       TCGA-99-7458       TCGA-MN-A4N4 
"ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" "ZNF556 WILD-TYPE" 
      TCGA-MN-A4N5 
"ZNF556 WILD-TYPE" 
                  vv
clus               LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ZNF556 MUTATED                            2                                 3
  ZNF556 WILD-TYPE                         15                                99
                  vv
clus               LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ZNF556 MUTATED                                                    5
  ZNF556 WILD-TYPE                                                291
                  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                                       15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              291
  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 306  10   4  25
D76V13, multiclass
    clus
vv   ZNF556 MUTATED ZNF556 WILD-TYPE
  R0              6              306
  R1              2               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
  ZNF556 MUTATED                                  0     0
  ZNF556 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF556 MUTATED                           1     9
  ZNF556 WILD-TYPE                        29   369
D76V14, multiclass
                                  clus
vv                                 ZNF556 MUTATED ZNF556 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0                7
  BLACK OR AFRICAN AMERICAN                     1               29
  WHITE                                         9              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"
D76V15, binary
                  cls
clus                 0   1
  ZNF556 MUTATED     0   8
  ZNF556 WILD-TYPE   6 343
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF556 MUTATED      0    8
  ZNF556 WILD-TYPE    6  343
                        clus
vv                       ZNF556 MUTATED ZNF556 WILD-TYPE
  HISPANIC OR LATINO                  0                6
  NOT HISPANIC OR LATINO              8              343
[1] 2 2
[1] FALSE

Clustering(77) Variable = ASCL3 MUTATION ANALYSIS
D77V1, survival
                 sevent
clus2               0   1
  ASCL3 MUTATED     4   3
  ASCL3 WILD-TYPE 294 168
  ASCL3 MUTATED ASCL3 WILD-TYPE 
              7             462 
  ASCL3 MUTATED ASCL3 WILD-TYPE 
              3             168 
$`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        17.79        19.99        24.23 
TCGA-95-7039 
       41.82 

$`ASCL3 WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 
       14.01         9.96        20.05         9.01        26.01        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       15.02        28.41        35.28        11.64        14.73        26.30 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       38.10        23.93        27.78        86.01        18.31        29.00 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       29.23         9.37        11.08        46.72        16.04        17.16 
TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 
       11.64        40.60        21.47        41.69        23.05        48.62 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        5.79         7.79         7.99        16.01        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       21.44         6.15        19.66        19.73        17.98        16.93 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       19.69        32.12        18.15        13.68        16.93        22.65 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       20.58        19.59        20.19        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       13.71        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        10.09        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         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-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       55.33        22.26        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
       78.67         8.45        48.46        60.72        57.53        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99        36.79        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       30.54        13.94        35.21        30.58        14.30        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        5.62        42.51        40.73        15.25        46.03        53.65 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26        31.30        28.67        20.02 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       27.09        32.71        22.03         3.91        23.15        25.41 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 
       15.39        18.64        11.28        34.19        17.65        18.44 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 
       19.82        29.23        29.72        15.19        23.08         5.06 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.72        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       19.96        26.01        17.10        17.62        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       12.33        20.71        21.40         3.25         0.92        15.81 
TCGA-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-64-1679 
       13.61        39.25        40.96        29.92        56.81        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         4.41        13.41        13.51        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 
       13.45         4.24        19.43         8.42         6.90        23.38 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
       50.33        66.64        77.85        43.82        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       36.66       108.66       100.57       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        9.57       104.19       238.29        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59       110.50        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-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-91-6840 
       10.62        41.36         1.97        10.19         2.60        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45        17.46        23.61         1.08        19.00 
TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 
       18.67        12.39        27.29         2.76        19.89        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        61.48        25.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       15.91        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       14.30        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 
       18.08        35.47        32.48        19.00        14.30        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.85         5.49        41.59        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        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        47.08         0.49         0.43        19.82        59.11 

  ASCL3 MUTATED ASCL3 WILD-TYPE 
           8.02            0.00 
  ASCL3 MUTATED ASCL3 WILD-TYPE 
          41.82          238.29 
  ASCL3 MUTATED ASCL3 WILD-TYPE 
          19.96           21.52 
[1] "8.0 - 41.8 (20.0)"  "0.0 - 238.3 (21.5)"
[1] "hr=" "1.7"
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      120      130        46        64         70
                 vv
clus              STAGE IIIB STAGE IV
  ASCL3 MUTATED            0        2
  ASCL3 WILD-TYPE         11       22
D77V3, multiclass
            clus
vv           ASCL3 MUTATED ASCL3 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             120
  STAGE IB               2             130
  STAGE IIA              0              46
  STAGE IIB              2              64
  STAGE IIIA             0              70
  STAGE IIIB             0              11
  STAGE IV               2              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
  ASCL3 MUTATED     1   4   2   0
  ASCL3 WILD-TYPE 155 257  41  18
D77V4, multiclass
    clus
vv   ASCL3 MUTATED ASCL3 WILD-TYPE
  T1             1             155
  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 302  89    72
D77V5, multiclass
       clus
vv      ASCL3 MUTATED ASCL3 WILD-TYPE
  N0                6             302
  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 258 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASCL3 MUTATED      2    5
  ASCL3 WILD-TYPE  258  216
        clus
vv       ASCL3 MUTATED ASCL3 WILD-TYPE
  FEMALE             2             258
  MALE               5             216
[1] 2 2
[1] FALSE
D77V8, binary
                 cls
clus                0   1
  ASCL3 MUTATED     5   2
  ASCL3 WILD-TYPE 379  53
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASCL3 MUTATED      5    2
  ASCL3 WILD-TYPE  379   53
     clus
vv    ASCL3 MUTATED ASCL3 WILD-TYPE
  NO              5             379
  YES             2              53
[1] 2 2
[1] FALSE
D77V9, continuous
[1] "Remove cluster labels:" "ASCL3 MUTATED"         
clus
  ASCL3 MUTATED ASCL3 WILD-TYPE 
              1             121 
     TCGA-44-6147      TCGA-44-A47F      TCGA-49-6742      TCGA-55-7573 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7914      TCGA-55-8205      TCGA-55-8511 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8621      TCGA-55-A491      TCGA-55-A492 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-64-1677      TCGA-73-4662      TCGA-73-7498      TCGA-93-8067 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-35-4122      TCGA-35-4123      TCGA-35-5375 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-3396      TCGA-44-3918      TCGA-44-4112      TCGA-44-6144 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-7660      TCGA-49-4486      TCGA-49-4494 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-49-4505      TCGA-49-4506      TCGA-49-4510      TCGA-49-6743 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-49-6744      TCGA-53-7624      TCGA-53-A4EZ      TCGA-55-5899 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7574      TCGA-55-7910      TCGA-55-7913 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-7995      TCGA-55-8089      TCGA-55-8096      TCGA-55-8208 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-8507      TCGA-55-8508      TCGA-55-8512      TCGA-55-8513 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-8620      TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A494 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-62-8394      TCGA-62-8395      TCGA-62-8397      TCGA-62-8398 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-62-8399      TCGA-62-8402      TCGA-62-A46O      TCGA-62-A46P 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-62-A46R      TCGA-62-A46S      TCGA-62-A46U      TCGA-62-A46V 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-62-A46Y      TCGA-62-A470      TCGA-62-A471      TCGA-62-A472 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-64-1681      TCGA-64-5775      TCGA-64-5778      TCGA-69-7974 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-69-8254      TCGA-71-6725      TCGA-71-8520      TCGA-73-4659 
"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-73-7499      TCGA-75-5122      TCGA-83-5908 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-6562      TCGA-86-6851      TCGA-86-7701      TCGA-86-7711 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-7713      TCGA-86-7714      TCGA-86-7953      TCGA-86-7954 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-7955      TCGA-86-8054      TCGA-86-8055      TCGA-86-8056 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-8073      TCGA-86-8074      TCGA-86-8075      TCGA-86-8076 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-8278      TCGA-86-8279      TCGA-86-8280      TCGA-86-8281 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-8358      TCGA-86-8359      TCGA-86-8668      TCGA-86-8669 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-8671      TCGA-86-A456      TCGA-86-A4P7      TCGA-91-6829 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-91-6849      TCGA-93-7347      TCGA-93-7348      TCGA-93-A4JN 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-93-A4JO      TCGA-95-7567      TCGA-99-7458      TCGA-MN-A4N4 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-MN-A4N5 
"ASCL3 WILD-TYPE" 
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ASCL3 MUTATED                            0                                 3
  ASCL3 WILD-TYPE                         17                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ASCL3 MUTATED                                                    4
  ASCL3 WILD-TYPE                                                292
                 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                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               99
  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"
D77V11, continuous
D77V12, continuous
[1] "Remove cluster labels:" "ASCL3 MUTATED"         
clus
  ASCL3 MUTATED ASCL3 WILD-TYPE 
              1             257 
     TCGA-05-4384      TCGA-05-4396      TCGA-05-4405      TCGA-05-4410 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-05-4427      TCGA-05-5420      TCGA-38-7271      TCGA-44-6147 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-6776      TCGA-44-7661      TCGA-44-7670      TCGA-44-8119 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-A47F      TCGA-55-1592      TCGA-55-1595      TCGA-55-7724 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7726      TCGA-55-7914      TCGA-55-8205 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-8511      TCGA-55-8621      TCGA-55-A48X      TCGA-55-A491 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-A492      TCGA-64-1677      TCGA-73-4662      TCGA-73-7498 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7166      TCGA-78-7633      TCGA-78-8660      TCGA-80-5607 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-91-6836      TCGA-91-A4BC      TCGA-93-8067      TCGA-93-A4JQ 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-95-7043      TCGA-95-7562      TCGA-95-7947      TCGA-95-7948 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-95-A4VK      TCGA-95-A4VN      TCGA-97-8172      TCGA-97-A4LX 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-97-A4M2      TCGA-97-A4M3      TCGA-97-A4M7      TCGA-J2-8194 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-L9-A443      TCGA-L9-A444      TCGA-MN-A4N1      TCGA-MP-A4T8 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-MP-A4TA      TCGA-MP-A4TC      TCGA-05-4390      TCGA-05-4415 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-05-4417      TCGA-05-4424      TCGA-05-4433      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-A44F 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-2656      TCGA-44-2657      TCGA-44-3396      TCGA-44-3398 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-3918      TCGA-44-4112      TCGA-44-5644      TCGA-44-5645 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-6144      TCGA-44-6145      TCGA-44-6148      TCGA-44-6774 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-6777      TCGA-44-6778      TCGA-44-6779 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-7659      TCGA-44-7660      TCGA-44-7662      TCGA-44-7667 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-7669      TCGA-44-7672      TCGA-44-8117      TCGA-44-8120 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-A479      TCGA-44-A47A      TCGA-44-A47B      TCGA-44-A47G 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-44-A4SS      TCGA-44-A4SU      TCGA-49-4486      TCGA-49-4494 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-49-4505      TCGA-53-7624      TCGA-53-7626      TCGA-53-7813 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-53-A4EZ      TCGA-55-5899      TCGA-55-6642      TCGA-55-6712 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-6971      TCGA-55-7227      TCGA-55-7283      TCGA-55-7570 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-7574      TCGA-55-7576      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-55-7913      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-55-8299 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-8301      TCGA-55-8302      TCGA-55-8506      TCGA-55-8507 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-8512      TCGA-55-8514      TCGA-55-8615      TCGA-55-8620 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-A48Y      TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A493 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-55-A494      TCGA-62-8398      TCGA-64-1681      TCGA-64-5774 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-64-5775      TCGA-64-5778      TCGA-64-5779      TCGA-64-5781 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-69-7761      TCGA-69-7763      TCGA-69-7764      TCGA-69-7765 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-69-7974      TCGA-69-7979      TCGA-69-8253      TCGA-69-8255 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-69-A59K      TCGA-73-4659      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-75-6214 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-75-7025      TCGA-75-7027      TCGA-75-7031      TCGA-78-7145 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7146      TCGA-78-7147      TCGA-78-7148      TCGA-78-7149 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7150      TCGA-78-7152      TCGA-78-7153      TCGA-78-7154 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7155      TCGA-78-7156      TCGA-78-7158      TCGA-78-7159 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7160      TCGA-78-7161      TCGA-78-7162      TCGA-78-7163 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7167      TCGA-78-7220      TCGA-78-7535      TCGA-78-7536 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-7537      TCGA-78-7539      TCGA-78-7542      TCGA-78-8640 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-78-8648      TCGA-78-8655      TCGA-78-8662      TCGA-80-5608 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-83-5908      TCGA-86-6851      TCGA-86-7711      TCGA-86-7714 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-7954      TCGA-86-8054      TCGA-86-8055      TCGA-86-8056 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-8073      TCGA-86-8074      TCGA-86-8281      TCGA-86-8358 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-8359      TCGA-86-8669      TCGA-86-8673      TCGA-86-8674 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-86-A456      TCGA-91-6829      TCGA-91-6830      TCGA-91-6840 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-91-6849      TCGA-91-8499      TCGA-93-7347      TCGA-93-7348 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-93-A4JN      TCGA-93-A4JO      TCGA-95-7567      TCGA-95-7944 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-95-A4VP      TCGA-97-7546      TCGA-97-7553      TCGA-97-7554 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-97-7941      TCGA-97-8171      TCGA-97-8174      TCGA-97-8176 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-97-8179      TCGA-97-A4M0      TCGA-97-A4M1      TCGA-97-A4M5 
"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-A4AD      TCGA-J2-A4AG      TCGA-L4-A4E5      TCGA-L4-A4E6 
"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-A4T9 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-MP-A4TE      TCGA-MP-A4TF      TCGA-MP-A4TH      TCGA-MP-A4TI 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-MP-A4TK      TCGA-MP-A5C7      TCGA-NJ-A4YG      TCGA-NJ-A4YI 
"ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" "ASCL3 WILD-TYPE" 
     TCGA-O1-A52J 
"ASCL3 WILD-TYPE" 
                 vv
clus               R0  R1  R2  RX
  ASCL3 MUTATED     4   0   1   0
  ASCL3 WILD-TYPE 308  12   3  25
D77V13, multiclass
    clus
vv   ASCL3 MUTATED ASCL3 WILD-TYPE
  R0             4             308
  R1             0              12
  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                        30   373
D77V14, multiclass
                                  clus
vv                                 ASCL3 MUTATED ASCL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    0              30
  WHITE                                        5             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"
D77V15, binary
                 cls
clus                0   1
  ASCL3 MUTATED     0   5
  ASCL3 WILD-TYPE   6 346
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASCL3 MUTATED      0    5
  ASCL3 WILD-TYPE    6  346
                        clus
vv                       ASCL3 MUTATED ASCL3 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             5             346
[1] 2 2
[1] FALSE

Clustering(78) Variable = DSG3 MUTATION ANALYSIS
D78V1, survival
                sevent
clus2              0   1
  DSG3 MUTATED    18  15
  DSG3 WILD-TYPE 280 156
  DSG3 MUTATED DSG3 WILD-TYPE 
            33            436 
  DSG3 MUTATED DSG3 WILD-TYPE 
            15            156 
$`DSG3 MUTATED`
TCGA-05-4382 TCGA-50-5932 TCGA-55-1592 TCGA-55-8511 TCGA-95-7948 TCGA-05-4430 
       19.96        40.60        23.05        18.15        15.65        25.02 
TCGA-05-5425 TCGA-44-2656 TCGA-44-6777 TCGA-44-7669 TCGA-44-A47G TCGA-50-5930 
       29.00        46.98        32.45        18.87        11.54         9.27 
TCGA-50-5936 TCGA-50-6590 TCGA-50-6594 TCGA-53-7626 TCGA-55-6981 TCGA-55-7911 
        8.45        42.35        12.16        30.54        45.34        17.65 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8506 TCGA-55-8508 TCGA-55-A490 TCGA-69-7974 
       19.82        29.72         0.36        20.28         3.25         6.05 
TCGA-69-A59K TCGA-73-4670 TCGA-78-7161 TCGA-86-A4JF TCGA-91-6829 TCGA-97-A4M0 
       19.43         4.31         9.57        24.23        41.36        21.44 
TCGA-99-8032 TCGA-NJ-A4YI TCGA-NJ-A55A 
        1.45         0.13         0.49 

$`DSG3 WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       14.01         9.96         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5935 TCGA-50-6597 TCGA-55-1595 TCGA-55-6978 
       17.16        11.64        21.47        41.69        48.62         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.79         7.99        16.01        23.18        14.53        21.44 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 
        6.15        19.66        19.73        17.98        16.93        19.69 
TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 
       32.12        13.68        16.93        22.65        20.58        19.59 
TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 
       20.19        20.65        13.87        52.60        82.68        39.09 
TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 
        8.48        50.24        10.55        85.32        13.71        16.18 
TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 
        1.45         6.12        17.29        16.54         2.86        15.68 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       21.40        18.18        17.92        20.19        20.52        17.75 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       20.68        24.30        23.80         6.35        10.09        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
        5.29        31.23         2.43        10.09        50.07         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
       45.01        37.02         0.00        24.03        47.05        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 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-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 
       26.01        25.02        24.00         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-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2665 
       37.71        49.05        44.61         4.37        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-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       23.18        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       36.07        23.64        12.66         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
        9.44        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-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 
       29.75        55.89        53.29        55.33        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47       101.72        15.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
        8.22        14.27        78.67        15.12        48.46        60.72 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 
       57.53        53.16         3.91        25.55        11.05         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99        36.79        27.25        34.29 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       13.94        35.21        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       69.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
       70.26        31.30        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 
       22.03         3.91        23.15        25.41        15.39        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7913 TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 
       11.28        34.19        18.44        29.23        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 
       15.42        17.56        15.72        14.47        13.74        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       19.96        26.01        17.10        17.62        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
       12.33        20.71        21.40         0.92        15.81        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-64-1679 
       13.61        39.25        40.96        29.92        56.81        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       38.37        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        7.56         4.41        13.41        13.51        14.01        13.45 
TCGA-69-8255 TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
        4.24         8.42         6.90        23.38        26.30        15.35 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       30.31         9.24         1.25        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 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-78-7162 TCGA-78-7163 TCGA-78-7167 
        5.88        64.90        22.92       104.19       238.29        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
       10.55       232.18        39.75        77.59       110.50        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 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        11.61        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-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-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.18        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
       19.00        41.82        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M1 
       15.39        16.41        14.30        21.60        20.58        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 
       20.84        18.67        24.56        34.85        36.76        21.57 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 
       18.08        35.47        32.48        19.00        14.30        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.85         5.49        41.59        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        74.33         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
       47.08         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 
        19.430         21.765 
[1] "0.1 - 47.0 (19.4)"  "0.0 - 238.3 (21.8)"
[1] "hr=" "2"  
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      116      122        42        59         64
                vv
clus             STAGE IIIB STAGE IV
  DSG3 MUTATED            0        1
  DSG3 WILD-TYPE         11       23
D78V3, multiclass
            clus
vv           DSG3 MUTATED DSG3 WILD-TYPE
  STAGE I               0              4
  STAGE IA              5            116
  STAGE IB             10            122
  STAGE IIA             4             42
  STAGE IIB             7             59
  STAGE IIIA            6             64
  STAGE IIIB            0             11
  STAGE IV              1             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
  DSG3 MUTATED     7  20   6   0
  DSG3 WILD-TYPE 149 241  37  18
D78V4, multiclass
    clus
vv   DSG3 MUTATED DSG3 WILD-TYPE
  T1            7            149
  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 287  84    66
D78V5, multiclass
       clus
vv      DSG3 MUTATED DSG3 WILD-TYPE
  N0              21            287
  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 241 207
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED     19   14
  DSG3 WILD-TYPE  241  207
        clus
vv       DSG3 MUTATED DSG3 WILD-TYPE
  FEMALE           19            241
  MALE             14            207
[1] 2 2
[1] FALSE
D78V8, binary
                cls
clus               0   1
  DSG3 MUTATED    25   6
  DSG3 WILD-TYPE 359  49
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED     25    6
  DSG3 WILD-TYPE  359   49
     clus
vv    DSG3 MUTATED DSG3 WILD-TYPE
  NO            25            359
  YES            6             49
[1] 2 2
[1] FALSE
D78V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DSG3 MUTATED                            0                                 9
  DSG3 WILD-TYPE                         17                                93
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DSG3 MUTATED                                                   19
  DSG3 WILD-TYPE                                                277
                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                                     17
  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                                  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 293  11   4  25
D78V13, multiclass
    clus
vv   DSG3 MUTATED DSG3 WILD-TYPE
  R0           19            293
  R1            1             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
  DSG3 MUTATED                                  0     0
  DSG3 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DSG3 MUTATED                           4    26
  DSG3 WILD-TYPE                        26   352
D78V14, multiclass
                                  clus
vv                                 DSG3 MUTATED DSG3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   4             26
  WHITE                                      26            352
[1] 4 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   6 324
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG3 MUTATED      0   27
  DSG3 WILD-TYPE    6  324
                        clus
vv                       DSG3 MUTATED DSG3 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           27            324
[1] 2 2
[1] FALSE

Clustering(79) Variable = C5AR1 MUTATION ANALYSIS
D79V1, survival
                 sevent
clus2               0   1
  C5AR1 MUTATED     4   2
  C5AR1 WILD-TYPE 294 169
  C5AR1 MUTATED C5AR1 WILD-TYPE 
              6             463 
  C5AR1 MUTATED C5AR1 WILD-TYPE 
              2             169 
$`C5AR1 MUTATED`
TCGA-05-4427 TCGA-05-5420 TCGA-73-4658 TCGA-55-7913 TCGA-86-8358 TCGA-97-7937 
       26.01        15.02        52.60        18.44        21.47        18.54 

$`C5AR1 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4434 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       15.02        28.41        35.28        11.64        14.73        26.30 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       38.10        23.93        27.78        86.01        18.31        29.00 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       29.23         9.37        11.08        46.72        16.04        17.16 
TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 
       11.64        40.60        21.47        41.69        23.05        48.62 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        5.79         7.79         7.99        16.01        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       21.44         6.15        19.66        19.73        17.98        16.93 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       19.69        32.12        18.15        13.68        16.93        22.65 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4662 
       20.58        19.59        20.19        20.65        13.87        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 
       39.09         8.48        50.24        10.55        85.32        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       16.18         1.45         6.12        17.29        16.54         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       15.68        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       10.09        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       47.05        19.00         2.99        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-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-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 
       44.61         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-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        48.46        60.72        57.53        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99        36.79        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       30.54        13.94        35.21        30.58        14.30        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        5.62        42.51        40.73        15.25        46.03        53.65 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26        31.30        28.67        20.02 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       27.09        32.71        22.03         3.91        23.15        25.41 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 
       15.39        18.64        11.28        34.19        17.65        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       29.23        29.72        15.19        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.72        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       19.96        26.01        17.10        17.62        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       12.33        20.71        21.40         3.25         0.92        15.81 
TCGA-55-A4DG TCGA-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-64-1679 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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        19.43         8.42         6.90 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       23.38        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
        1.25        50.33        66.64        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       49.84        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
       22.92         9.57       104.19       238.29        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 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        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.18        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
       19.00        41.82        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59        15.91        18.67         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.57        18.08        35.47        32.48        19.00        14.30 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        47.08         0.49         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  C5AR1 MUTATED C5AR1 WILD-TYPE 
          15.02            0.00 
  C5AR1 MUTATED C5AR1 WILD-TYPE 
          52.60          238.29 
  C5AR1 MUTATED C5AR1 WILD-TYPE 
         20.005          21.470 
[1] "15.0 - 52.6 (20.0)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1"  
D79V2, continuous
                 vv
clus              STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  C5AR1 MUTATED         0        1        3         0         1          1
  C5AR1 WILD-TYPE       4      120      129        46        65         69
                 vv
clus              STAGE IIIB STAGE IV
  C5AR1 MUTATED            0        0
  C5AR1 WILD-TYPE         11       24
D79V3, multiclass
            clus
vv           C5AR1 MUTATED C5AR1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               1             120
  STAGE IB               3             129
  STAGE IIA              0              46
  STAGE IIB              1              65
  STAGE IIIA             1              69
  STAGE IIIB             0              11
  STAGE IV               0              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
  C5AR1 MUTATED     1   5   0   0
  C5AR1 WILD-TYPE 155 256  43  18
D79V4, multiclass
    clus
vv   C5AR1 MUTATED C5AR1 WILD-TYPE
  T1             1             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     4   1     1
  C5AR1 WILD-TYPE 304  88    71
D79V5, multiclass
       clus
vv      C5AR1 MUTATED C5AR1 WILD-TYPE
  N0                4             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     3   3
  C5AR1 WILD-TYPE 257 218
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C5AR1 MUTATED      3    3
  C5AR1 WILD-TYPE  257  218
        clus
vv       C5AR1 MUTATED C5AR1 WILD-TYPE
  FEMALE             3             257
  MALE               3             218
[1] 2 2
[1] FALSE
D79V8, binary
                 cls
clus                0   1
  C5AR1 MUTATED     5   0
  C5AR1 WILD-TYPE 379  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C5AR1 MUTATED      5    0
  C5AR1 WILD-TYPE  379   55
     clus
vv    C5AR1 MUTATED C5AR1 WILD-TYPE
  NO              5             379
  YES             0              55
[1] 2 2
[1] FALSE
D79V9, continuous
[1] "Remove cluster labels:" "C5AR1 MUTATED"         
clus
  C5AR1 MUTATED C5AR1 WILD-TYPE 
              2             120 
     TCGA-44-6147      TCGA-44-A47F      TCGA-49-6742      TCGA-55-7573 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-55-7725      TCGA-55-7914      TCGA-55-8205      TCGA-55-8511 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-55-8619      TCGA-55-8621      TCGA-55-A491      TCGA-55-A492 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-64-1677      TCGA-73-4662      TCGA-73-7498      TCGA-93-8067 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-MN-A4N1      TCGA-35-4122      TCGA-35-4123      TCGA-35-5375 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-44-3396      TCGA-44-3918      TCGA-44-4112      TCGA-44-6144 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-44-6775      TCGA-44-7660      TCGA-49-4486      TCGA-49-4494 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-49-4505      TCGA-49-4506      TCGA-49-4510      TCGA-49-6743 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-49-6744      TCGA-53-7624      TCGA-53-A4EZ      TCGA-55-5899 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-55-7283      TCGA-55-7574      TCGA-55-7910      TCGA-55-7995 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-55-8089      TCGA-55-8096      TCGA-55-8208      TCGA-55-8507 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-55-8508      TCGA-55-8512      TCGA-55-8513      TCGA-55-8620 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-55-A48Z      TCGA-55-A490      TCGA-55-A494      TCGA-62-8394 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-62-8395      TCGA-62-8397      TCGA-62-8398      TCGA-62-8399 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-62-8402      TCGA-62-A46O      TCGA-62-A46P      TCGA-62-A46R 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-62-A46S      TCGA-62-A46U      TCGA-62-A46V      TCGA-62-A46Y 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-62-A470      TCGA-62-A471      TCGA-62-A472      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-73-4666 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-73-4668      TCGA-73-4670      TCGA-73-4676      TCGA-73-4677 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-73-7499      TCGA-75-5122      TCGA-83-5908      TCGA-86-6562 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-86-6851      TCGA-86-7701      TCGA-86-7711      TCGA-86-7713 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-86-7714      TCGA-86-7953      TCGA-86-7954      TCGA-86-7955 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-86-8054      TCGA-86-8055      TCGA-86-8056      TCGA-86-8073 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-86-8074      TCGA-86-8075      TCGA-86-8076      TCGA-86-8278 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-86-8279      TCGA-86-8280      TCGA-86-8281      TCGA-86-8359 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-86-8668      TCGA-86-8669      TCGA-86-8671      TCGA-86-A456 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-86-A4JF      TCGA-86-A4P7      TCGA-91-6829      TCGA-91-6849 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-93-7347      TCGA-93-7348      TCGA-93-A4JN      TCGA-93-A4JO 
"C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" "C5AR1 WILD-TYPE" 
     TCGA-95-7567      TCGA-99-7458      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                         17                               101
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  C5AR1 MUTATED                                                    4
  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)             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                                                   C5AR1 WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              101
  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     5   0   0   0
  C5AR1 WILD-TYPE 307  12   4  25
D79V13, multiclass
    clus
vv   C5AR1 MUTATED C5AR1 WILD-TYPE
  R0             5             307
  R1             0              12
  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                           1     3
  C5AR1 WILD-TYPE                        29   375
D79V14, multiclass
                                  clus
vv                                 C5AR1 MUTATED C5AR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              29
  WHITE                                        3             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"
D79V15, binary
                 cls
clus                0   1
  C5AR1 MUTATED     0   4
  C5AR1 WILD-TYPE   6 347
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C5AR1 MUTATED      0    4
  C5AR1 WILD-TYPE    6  347
                        clus
vv                       C5AR1 MUTATED C5AR1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             4             347
[1] 2 2
[1] FALSE

Clustering(80) Variable = ASXL2 MUTATION ANALYSIS
D80V1, survival
                 sevent
clus2               0   1
  ASXL2 MUTATED    11   7
  ASXL2 WILD-TYPE 287 164
  ASXL2 MUTATED ASXL2 WILD-TYPE 
             18             451 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
              7             164 
$`ASXL2 MUTATED`
TCGA-05-4396 TCGA-44-8119 TCGA-95-7947 TCGA-05-4430 TCGA-44-3398 TCGA-55-6972 
        9.96         9.37        15.68        25.02        38.24        53.65 
TCGA-55-6984 TCGA-55-7574 TCGA-55-8302 TCGA-55-8620 TCGA-55-A493 TCGA-64-5781 
       24.99        32.71        15.72        12.33         0.92        51.25 
TCGA-71-8520 TCGA-78-8640 TCGA-86-8054 TCGA-86-A4JF TCGA-91-6831 TCGA-NJ-A4YP 
        6.90       232.18        37.74        24.23        10.19         1.64 

$`ASXL2 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       29.00        29.23        11.08        46.72        16.04        17.16 
TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 
       11.64        40.60        21.47        41.69        23.05        48.62 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        5.79         7.79         7.99        16.01        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       21.44         6.15        19.66        19.73        17.98        16.93 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       19.69        32.12        18.15        13.68        16.93        22.65 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       20.58        19.59        20.19        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       13.71        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
        2.86        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       10.09        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       47.05        19.00         2.99        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 
       30.02        21.99        26.01        25.02        24.00         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-38-4632 
        8.68        97.74       120.79        37.71        49.05        44.61 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3918 
        4.37        46.98        44.42        42.77        37.15        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       19.56        23.15        21.63        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        22.72        19.46         7.17        36.07        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         8.55        15.98        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 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-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 
       29.75        55.89        53.29        55.33        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47       101.72        15.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
        8.22         9.27        14.27        78.67         8.45        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       48.46        60.72        57.53        53.16        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05        12.16         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99        36.79        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       35.21        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       40.73        15.25        46.03         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       32.71        92.81        40.54       107.21        70.26        31.30 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       28.67        20.02        27.09        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       25.41        15.39        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.44        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       15.42        17.56        14.47         0.36        13.74        20.28 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A494 TCGA-55-A4DG 
        1.58        20.71        21.40         3.25        15.81        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-64-1679 
       13.61        39.25        40.96        29.92        56.81        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 
       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-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        13.41        13.51        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
        4.24        19.43         8.42        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 
        4.31        30.31         9.24         1.25        50.33        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       77.85        43.82        85.15        49.84        36.66       108.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
      100.57       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-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      238.29        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       26.01        39.35        10.55        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
       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        11.61        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 
       13.64        26.47        10.62        41.36         1.97         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.18        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
       19.00        41.82        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       15.39        16.41        14.30        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       19.76        20.84        18.67        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        1.45        21.57        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       14.30        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE 
       37.35        86.04        58.85         5.49        41.59        29.46 
TCGA-MP-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 
       74.33         0.13        47.08         0.49         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  ASXL2 MUTATED ASXL2 WILD-TYPE 
           0.92            0.00 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
         232.18          238.29 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
         19.975          21.470 
[1] "0.9 - 232.2 (20.0)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.1"
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      119      123        45        62         70
                 vv
clus              STAGE IIIB STAGE IV
  ASXL2 MUTATED            1        1
  ASXL2 WILD-TYPE         10       23
D80V3, multiclass
            clus
vv           ASXL2 MUTATED ASXL2 WILD-TYPE
  STAGE I                0               4
  STAGE IA               2             119
  STAGE IB               9             123
  STAGE IIA              1              45
  STAGE IIB              4              62
  STAGE IIIA             0              70
  STAGE IIIB             1              10
  STAGE IV               1              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
  ASXL2 MUTATED     4  11   2   1
  ASXL2 WILD-TYPE 152 250  41  17
D80V4, multiclass
    clus
vv   ASXL2 MUTATED ASXL2 WILD-TYPE
  T1             4             152
  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 295  84    72
D80V5, multiclass
       clus
vv      ASXL2 MUTATED ASXL2 WILD-TYPE
  N0               13             295
  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 253 210
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED      7   11
  ASXL2 WILD-TYPE  253  210
        clus
vv       ASXL2 MUTATED ASXL2 WILD-TYPE
  FEMALE             7             253
  MALE              11             210
[1] 2 2
[1] FALSE
D80V8, binary
                 cls
clus                0   1
  ASXL2 MUTATED    12   3
  ASXL2 WILD-TYPE 372  52
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED     12    3
  ASXL2 WILD-TYPE  372   52
     clus
vv    ASXL2 MUTATED ASXL2 WILD-TYPE
  NO             12             372
  YES             3              52
[1] 2 2
[1] FALSE
D80V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ASXL2 MUTATED                            1                                 4
  ASXL2 WILD-TYPE                         16                                98
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ASXL2 MUTATED                                                   11
  ASXL2 WILD-TYPE                                                285
                 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                                      16
  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                                   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 299  11   4  25
D80V13, multiclass
    clus
vv   ASXL2 MUTATED ASXL2 WILD-TYPE
  R0            13             299
  R1             1              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
  ASXL2 MUTATED                                  0     1
  ASXL2 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ASXL2 MUTATED                           0    14
  ASXL2 WILD-TYPE                        30   364
D80V14, multiclass
                                  clus
vv                                 ASXL2 MUTATED ASXL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    0              30
  WHITE                                       14             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"
D80V15, binary
                 cls
clus                0   1
  ASXL2 MUTATED     0  14
  ASXL2 WILD-TYPE   6 337
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED      0   14
  ASXL2 WILD-TYPE    6  337
                        clus
vv                       ASXL2 MUTATED ASXL2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            14             337
[1] 2 2
[1] FALSE

Clustering(81) Variable = DLX5 MUTATION ANALYSIS
D81V1, survival
                sevent
clus2              0   1
  DLX5 MUTATED     6   7
  DLX5 WILD-TYPE 292 164
  DLX5 MUTATED DLX5 WILD-TYPE 
            13            456 
  DLX5 MUTATED DLX5 WILD-TYPE 
             7            164 
$`DLX5 MUTATED`
TCGA-95-7043 TCGA-MP-A4TA TCGA-38-4625 TCGA-50-6593 TCGA-55-8089 TCGA-55-8299 
       16.54        31.23        97.74        11.05        23.08        15.42 
TCGA-55-8514 TCGA-86-6851 TCGA-86-8054 TCGA-91-6828 TCGA-J2-A4AD TCGA-MP-A4T9 
       17.10         5.88        37.74        10.62        18.08        41.59 
TCGA-NJ-A4YQ 
       47.08 

$`DLX5 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       17.29         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TC 
       23.80         6.35        10.09        27.19         5.29         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 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-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 
       44.61         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-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       32.45        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        48.46        60.72        57.53        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
       42.35         3.91        25.55        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99        36.79        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        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
      107.21        70.26        31.30        28.67        20.02        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
       32.71        22.03         3.91        23.15        25.41        15.39 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       18.64        11.28        34.19        17.65        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       29.23        29.72        15.19         5.06        17.79        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       15.65        29.19        22.16        17.56        15.72        14.47 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36        13.74        20.28        17.72        19.96        26.01 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.62        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        3.25         0.92        15.81        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 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-69-7760 
       18.84        14.04        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41        13.41        13.51        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       19.43         8.42         6.90        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 
        4.31        30.31         9.24         1.25        50.33        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       77.85        43.82        85.15        49.84        36.66       108.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
      100.57       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-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      238.29        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       26.01        39.35        10.55       232.18        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 
      110.50        93.11        27.09        12.36        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
       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        11.61        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       24.23        13.64        26.47        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
        1.08        19.00        41.82        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       25.48        18.54         0.59        15.91        18.67         5.39 
TCGA-97-8175 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-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       36.76         1.45        21.57        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       14.30        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF 
       37.35        86.04        58.85         5.49        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.13         1.64         0.49         0.43        19.82        59.11 

  DLX5 MUTATED DLX5 WILD-TYPE 
          5.88           0.00 
  DLX5 MUTATED DLX5 WILD-TYPE 
         97.74         238.29 
  DLX5 MUTATED DLX5 WILD-TYPE 
         18.08          21.47 
[1] "5.9 - 97.7 (18.1)"  "0.0 - 238.3 (21.5)"
[1] "hr=" "1.5"
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      114      130        45        65         68
                vv
clus             STAGE IIIB STAGE IV
  DLX5 MUTATED            0        0
  DLX5 WILD-TYPE         11       24
D81V3, multiclass
            clus
vv           DLX5 MUTATED DLX5 WILD-TYPE
  STAGE I               0              4
  STAGE IA              7            114
  STAGE IB              2            130
  STAGE IIA             1             45
  STAGE IIB             1             65
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              0             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
  DLX5 MUTATED     9   4   0   0
  DLX5 WILD-TYPE 147 257  43  18
D81V4, multiclass
    clus
vv   DLX5 MUTATED DLX5 WILD-TYPE
  T1            9            147
  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 299  87    70
D81V5, multiclass
       clus
vv      DLX5 MUTATED DLX5 WILD-TYPE
  N0               9            299
  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 250 218
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLX5 MUTATED     10    3
  DLX5 WILD-TYPE  250  218
        clus
vv       DLX5 MUTATED DLX5 WILD-TYPE
  FEMALE           10            250
  MALE              3            218
[1] 2 2
[1] FALSE
D81V8, binary
                cls
clus               0   1
  DLX5 MUTATED    11   2
  DLX5 WILD-TYPE 373  53
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLX5 MUTATED     11    2
  DLX5 WILD-TYPE  373   53
     clus
vv    DLX5 MUTATED DLX5 WILD-TYPE
  NO            11            373
  YES            2             53
[1] 2 2
[1] FALSE
D81V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  DLX5 MUTATED                            1                                 3
  DLX5 WILD-TYPE                         16                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DLX5 MUTATED                                                    9
  DLX5 WILD-TYPE                                                287
                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                                     16
  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"
D81V11, continuous
D81V12, continuous
                vv
clus              R0  R1  R2  RX
  DLX5 MUTATED     8   0   0   3
  DLX5 WILD-TYPE 304  12   4  22
D81V13, multiclass
    clus
vv   DLX5 MUTATED DLX5 WILD-TYPE
  R0            8            304
  R1            0             12
  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                        29   366
D81V14, multiclass
                                  clus
vv                                 DLX5 MUTATED DLX5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             29
  WHITE                                      12            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"
D81V15, binary
                cls
clus               0   1
  DLX5 MUTATED     0  13
  DLX5 WILD-TYPE   6 338
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLX5 MUTATED      0   13
  DLX5 WILD-TYPE    6  338
                        clus
vv                       DLX5 MUTATED DLX5 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           13            338
[1] 2 2
[1] FALSE

Clustering(82) Variable = ATAD2 MUTATION ANALYSIS
D82V1, survival
                 sevent
clus2               0   1
  ATAD2 MUTATED    10   3
  ATAD2 WILD-TYPE 288 168
  ATAD2 MUTATED ATAD2 WILD-TYPE 
             13             456 
  ATAD2 MUTATED ATAD2 WILD-TYPE 
              3             168 
$`ATAD2 MUTATED`
TCGA-78-7633 TCGA-05-4397 TCGA-44-5644 TCGA-44-6144 TCGA-55-7994 TCGA-64-1679 
       50.24        24.03        28.37        23.77        19.82        81.80 
TCGA-64-5775 TCGA-69-7979 TCGA-69-7980 TCGA-95-7567 TCGA-97-7937 TCGA-99-8025 
        2.04        13.41        13.51        18.67        18.54        34.85 
TCGA-MN-A4N4 
       38.63 

$`ATAD2 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-8660 
       13.87        52.60        82.68        39.09         8.48        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
        0.00        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         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-44-5645 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       28.01        19.56        23.15        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
       61.28        16.44        22.72        19.46         7.17        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       18.87        23.64        12.66         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
        9.44        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 
       29.46        29.75        55.89        53.29        55.33        22.26 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       49.28         8.22         9.27        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       15.12        48.46        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
        3.91        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99        36.79        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       13.94        35.21        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
      107.21        70.26        31.30        28.67        20.02        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
       32.71        22.03         3.91        23.15        25.41        15.39 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7995 
       18.64        11.28        34.19        17.65        18.44        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       29.72        15.19        23.08         5.06        17.79        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       15.65        29.19        22.16        15.42        17.56        15.72 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
       14.47         0.36        13.74        20.28        17.72        19.96 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
       26.01        17.10        17.62        14.66         1.58        12.33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
       20.71        21.40         3.25         0.92        15.81        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 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-64-1681 
       13.61        39.25        40.96        29.92        56.81        38.37 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
       87.98        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-69-7760 
       18.84        14.04        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
        4.41        14.01        13.45         4.24        19.43         8.42 
TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        6.90        23.38        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
        9.24         1.25        50.33        66.64        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       85.15        49.84        36.66       108.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 
       64.90        22.92         9.57       104.19       238.29        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
       10.55       232.18        39.75        77.59       110.50        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 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        11.61        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        12.23        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7944 TCGA-95-8039 
       23.61         1.08        19.00        41.82        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       25.48         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       15.39        16.41        14.30        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
       19.76        20.84        18.67        24.56        36.76         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.57        18.08        35.47        32.48        19.00        14.30 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.85         5.49        41.59        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        19.13        73.91        71.05        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        1.64        47.08         0.49         0.43        19.82        59.11 

  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          21.455 
[1] "2.0 - 81.8 (23.8)"  "0.0 - 238.3 (21.5)"
[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      118      128        46        63         67
                 vv
clus              STAGE IIIB STAGE IV
  ATAD2 MUTATED            0        0
  ATAD2 WILD-TYPE         11       24
D82V3, multiclass
            clus
vv           ATAD2 MUTATED ATAD2 WILD-TYPE
  STAGE I                1               3
  STAGE IA               3             118
  STAGE IB               4             128
  STAGE IIA              0              46
  STAGE IIB              3              63
  STAGE IIIA             3              67
  STAGE IIIB             0              11
  STAGE IV               0              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
  ATAD2 MUTATED     5   6   2   1
  ATAD2 WILD-TYPE 151 255  41  17
D82V4, multiclass
    clus
vv   ATAD2 MUTATED ATAD2 WILD-TYPE
  T1             5             151
  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 299  87    70
D82V5, multiclass
       clus
vv      ATAD2 MUTATED ATAD2 WILD-TYPE
  N0                9             299
  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 255 212
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD2 MUTATED      5    9
  ATAD2 WILD-TYPE  255  212
        clus
vv       ATAD2 MUTATED ATAD2 WILD-TYPE
  FEMALE             5             255
  MALE               9             212
[1] 2 2
[1] FALSE
D82V8, binary
                 cls
clus                0   1
  ATAD2 MUTATED    11   0
  ATAD2 WILD-TYPE 373  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD2 MUTATED     11    0
  ATAD2 WILD-TYPE  373   55
     clus
vv    ATAD2 MUTATED ATAD2 WILD-TYPE
  NO             11             373
  YES             0              55
[1] 2 2
[1] FALSE
D82V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  ATAD2 MUTATED                            1                                 3
  ATAD2 WILD-TYPE                         16                                99
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ATAD2 MUTATED                                                    9
  ATAD2 WILD-TYPE                                                287
                 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                                      16
  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                               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 305  12   4  24
D82V13, multiclass
    clus
vv   ATAD2 MUTATED ATAD2 WILD-TYPE
  R0             7             305
  R1             0              12
  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                        29   366
D82V14, multiclass
                                  clus
vv                                 ATAD2 MUTATED ATAD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              29
  WHITE                                       12             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"
D82V15, binary
                 cls
clus                0   1
  ATAD2 MUTATED     0  12
  ATAD2 WILD-TYPE   6 339
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD2 MUTATED      0   12
  ATAD2 WILD-TYPE    6  339
                        clus
vv                       ATAD2 MUTATED ATAD2 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO            12             339
[1] 2 2
[1] FALSE

Clustering(83) Variable = RAF1 MUTATION ANALYSIS
D83V1, survival
                sevent
clus2              0   1
  RAF1 MUTATED     5   1
  RAF1 WILD-TYPE 293 170
  RAF1 MUTATED RAF1 WILD-TYPE 
             6            463 
  RAF1 MUTATED RAF1 WILD-TYPE 
             1            170 
$`RAF1 MUTATED`
TCGA-05-4427 TCGA-J2-8192 TCGA-55-8505 TCGA-69-7765 TCGA-78-7220 TCGA-97-7546 
       26.01        24.30        14.47         5.42        26.53        42.25 

$`RAF1 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8194 
       17.92        20.19        20.52        17.75        20.68        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        10.09        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         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-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       55.33        22.26        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       53.16        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 
       34.29        30.54        13.94        35.21        30.58        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       80.52         5.62        42.51        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       53.65         3.88        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26        31.30        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       20.02        27.09        32.71        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       25.41        15.39        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.44        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       15.42        17.56        15.72         0.36        13.74        20.28 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
        1.58        12.33        20.71        21.40         3.25         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       56.81        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-69-7760 TCGA-69-7761 TCGA-69-7763 
       14.73         5.72         4.64         6.64         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        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        19.43         8.42         6.90 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       23.38        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
        1.25        50.33        66.64        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       49.84        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 
       22.92         9.57       104.19       238.29        88.14        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59       110.50        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        35.24        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.18        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
       19.00        41.82        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       19.89        64.60        63.52        61.48        25.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59        15.91        18.67         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.57        18.08        35.47        32.48        19.00        14.30 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        47.08         0.49         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  RAF1 MUTATED RAF1 WILD-TYPE 
          5.42           0.00 
  RAF1 MUTATED RAF1 WILD-TYPE 
         42.25         238.29 
  RAF1 MUTATED RAF1 WILD-TYPE 
        25.155         21.440 
[1] "5.4 - 42.2 (25.2)"  "0.0 - 238.3 (21.4)"
[1] "hr=" "1.7"
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      120      132        45        65         68
                vv
clus             STAGE IIIB STAGE IV
  RAF1 MUTATED            0        0
  RAF1 WILD-TYPE         11       24
D83V3, multiclass
            clus
vv           RAF1 MUTATED RAF1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              1            120
  STAGE IB              0            132
  STAGE IIA             1             45
  STAGE IIB             1             65
  STAGE IIIA            2             68
  STAGE IIIB            0             11
  STAGE IV              0             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 154 258  43  17
D83V4, multiclass
    clus
vv   RAF1 MUTATED RAF1 WILD-TYPE
  T1            2            154
  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 306  87    70
D83V5, multiclass
       clus
vv      RAF1 MUTATED RAF1 WILD-TYPE
  N0               2            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"
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 256 219
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED      4    2
  RAF1 WILD-TYPE  256  219
        clus
vv       RAF1 MUTATED RAF1 WILD-TYPE
  FEMALE            4            256
  MALE              2            219
[1] 2 2
[1] FALSE
D83V8, binary
                cls
clus               0   1
  RAF1 MUTATED     4   2
  RAF1 WILD-TYPE 380  53
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED      4    2
  RAF1 WILD-TYPE  380   53
     clus
vv    RAF1 MUTATED RAF1 WILD-TYPE
  NO             4            380
  YES            2             53
[1] 2 2
[1] FALSE
D83V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  RAF1 MUTATED                            1                                 3
  RAF1 WILD-TYPE                         16                                99
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  RAF1 MUTATED                                                    2
  RAF1 WILD-TYPE                                                294
                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                                     16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)            294
  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 308  12   4  25
D83V13, multiclass
    clus
vv   RAF1 MUTATED RAF1 WILD-TYPE
  R0            4            308
  R1            0             12
  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                        29   374
D83V14, multiclass
                                  clus
vv                                 RAF1 MUTATED RAF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             29
  WHITE                                       4            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"
D83V15, binary
                cls
clus               0   1
  RAF1 MUTATED     0   4
  RAF1 WILD-TYPE   6 347
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED      0    4
  RAF1 WILD-TYPE    6  347
                        clus
vv                       RAF1 MUTATED RAF1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO            4            347
[1] 2 2
[1] FALSE

Clustering(84) Variable = A2M MUTATION ANALYSIS
D84V1, survival
               sevent
clus2             0   1
  A2M MUTATED    13   5
  A2M WILD-TYPE 285 166
  A2M MUTATED A2M WILD-TYPE 
           18           451 
  A2M MUTATED A2M WILD-TYPE 
            5           166 
$`A2M MUTATED`
TCGA-05-4402 TCGA-05-4405 TCGA-55-1595 TCGA-55-8203 TCGA-95-7043 TCGA-38-4632 
        8.02        20.05        48.62        17.98        16.54        44.61 
TCGA-55-8089 TCGA-55-A490 TCGA-64-1676 TCGA-64-5781 TCGA-69-7980 TCGA-73-4670 
       23.08         3.25        56.81        51.25        13.51         4.31 
TCGA-78-8640 TCGA-86-8054 TCGA-91-6828 TCGA-91-6848 TCGA-97-7554 TCGA-MN-A4N4 
      232.18        37.74        10.62         7.36        25.48        38.63 

$`A2M WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 
       19.96        14.01         9.96         9.01        26.01        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       15.02        28.41        35.28        11.64        14.73        26.30 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       38.10        23.93        27.78        86.01        18.31        29.00 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
       29.23         9.37        11.08        46.72        16.04        17.16 
TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-6978 
       11.64        40.60        21.47        41.69        23.05         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.79         7.99        16.01        23.18        14.53        21.44 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 
        6.15        19.66        19.73        16.93        19.69        32.12 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 
       18.15        13.68        16.93        22.65        20.58        19.59 
TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 
       20.19        20.65        13.87        52.60        82.68        39.09 
TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 
        8.48        50.24        10.55        85.32        13.71        16.18 
TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
        1.45         6.12        17.29         2.86        15.68        15.65 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       21.40        18.18        17.92        20.19        20.52        17.75 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       20.68        24.30        23.80         6.35        10.09        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
        5.29        31.23         2.43        10.09        50.07         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
       45.01        37.02         0.00        24.03        47.05        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       26.01        25.02        25.02        24.00         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 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-A44F TCGA-44-2656 
       97.74       120.79        37.71        49.05         4.37        46.98 
TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       44.42        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-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        23.18        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       22.72        19.46         7.17        36.07        18.87        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       12.66         8.55        15.98        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       35.54        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 
       55.89        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 
      101.72        15.72        60.16        47.41        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        9.27        14.27        78.67         8.45        15.12        48.46 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       60.72        57.53        53.16        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05        12.16         6.21         0.72        10.13        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.79        27.25        34.29        30.54        13.94        35.21 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       30.58        14.30        80.52         5.62        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       15.25        46.03        53.65         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       31.30        28.67        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        3.91        23.15        25.41        15.39        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       34.19        17.65        18.44        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       15.19         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       13.74        20.28        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.62        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       29.92        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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 
        5.42         7.56         6.05         4.41        13.41        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 
       13.45         4.24        19.43         8.42         6.90        23.38 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 
       26.30        15.35        30.31         9.24         1.25        50.33 
TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 
       66.64        77.85        43.82        85.15        49.84        36.66 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
      108.66       100.57       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      104.19       238.29        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 
       53.33        26.01        39.35        10.55        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
      110.50        93.11        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        11.61 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-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-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 
       10.19         2.60        12.23        27.68         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
        1.08        19.00        41.82        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       15.39        16.41        14.30        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       19.76        20.84        18.67        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        1.45        21.57        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       14.30         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        47.08         0.49         0.43        19.82 
TCGA-O1-A52J 
       59.11 

  A2M MUTATED A2M WILD-TYPE 
         3.25          0.00 
  A2M MUTATED A2M WILD-TYPE 
       232.18        238.29 
  A2M MUTATED A2M WILD-TYPE 
       21.565        21.470 
[1] "3.2 - 232.2 (21.6)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.5"
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      114      129        44        64         68
               vv
clus            STAGE IIIB STAGE IV
  A2M MUTATED            0        3
  A2M WILD-TYPE         11       21
D84V3, multiclass
            clus
vv           A2M MUTATED A2M WILD-TYPE
  STAGE I              1             3
  STAGE IA             7           114
  STAGE IB             3           129
  STAGE IIA            2            44
  STAGE IIB            2            64
  STAGE IIIA           2            68
  STAGE IIIB           0            11
  STAGE IV             3            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
  A2M MUTATED     9  10   1   0
  A2M WILD-TYPE 147 251  42  18
D84V4, multiclass
    clus
vv   A2M MUTATED A2M WILD-TYPE
  T1           9           147
  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 294  86    70
D84V5, multiclass
       clus
vv      A2M MUTATED A2M WILD-TYPE
  N0             14           294
  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 250 211
[1] "tbl2"
               cls
clus            [,1] [,2]
  A2M MUTATED     10   10
  A2M WILD-TYPE  250  211
        clus
vv       A2M MUTATED A2M WILD-TYPE
  FEMALE          10           250
  MALE            10           211
[1] 2 2
[1] FALSE
D84V8, binary
               cls
clus              0   1
  A2M MUTATED    20   0
  A2M WILD-TYPE 364  55
[1] "tbl2"
               cls
clus            [,1] [,2]
  A2M MUTATED     20    0
  A2M WILD-TYPE  364   55
     clus
vv    A2M MUTATED A2M WILD-TYPE
  NO           20           364
  YES           0            55
[1] 2 2
[1] FALSE
D84V9, continuous
               vv
clus            LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  A2M MUTATED                            1                                 4
  A2M WILD-TYPE                         16                                98
               vv
clus            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  A2M MUTATED                                                   13
  A2M WILD-TYPE                                                283
               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            16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                            4            98
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)          13           283
  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 297  12   3  25
D84V13, multiclass
    clus
vv   A2M MUTATED A2M WILD-TYPE
  R0          15           297
  R1           0            12
  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                        29   365
D84V14, multiclass
                                  clus
vv                                 A2M MUTATED A2M WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1             6
  BLACK OR AFRICAN AMERICAN                  1            29
  WHITE                                     13           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"
D84V15, binary
               cls
clus              0   1
  A2M MUTATED     0  15
  A2M WILD-TYPE   6 336
[1] "tbl2"
               cls
clus            [,1] [,2]
  A2M MUTATED      0   15
  A2M WILD-TYPE    6  336
                        clus
vv                       A2M MUTATED A2M WILD-TYPE
  HISPANIC OR LATINO               0             6
  NOT HISPANIC OR LATINO          15           336
[1] 2 2
[1] FALSE

Clustering(85) Variable = SND1 MUTATION ANALYSIS
D85V1, survival
                sevent
clus2              0   1
  SND1 MUTATED     9   7
  SND1 WILD-TYPE 289 164
  SND1 MUTATED SND1 WILD-TYPE 
            16            453 
  SND1 MUTATED SND1 WILD-TYPE 
             7            164 
$`SND1 MUTATED`
TCGA-78-7166 TCGA-95-7043 TCGA-95-7947 TCGA-05-4415 TCGA-44-3918 TCGA-50-5930 
        8.48        16.54        15.68         2.99        34.06         9.27 
TCGA-50-6594 TCGA-64-1676 TCGA-69-7978 TCGA-78-7155 TCGA-86-7701 TCGA-86-7955 
       12.16        56.81         4.41        38.50        31.13        35.24 
TCGA-86-8358 TCGA-86-8359 TCGA-91-6828 TCGA-NJ-A4YQ 
       21.47        14.60        10.62        47.08 

$`SND1 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       16.93        22.65        20.58        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7633 TCGA-78-8660 
       13.87        52.60        82.68        39.09        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7562 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
        2.86        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       10.09        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       47.05        19.00        14.96        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 
       21.99        26.01        25.02        25.02        24.00         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 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-38-4632 
        8.68        97.74       120.79        37.71        49.05        44.61 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
        4.37        46.98        44.42        42.77        37.15        38.24 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
       33.73        26.56        33.30        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       19.56        23.15        21.63        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        22.72        19.46         7.17        36.07        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         8.55        15.98        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 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-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 
       29.75        55.89        53.29        55.33        22.26        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47       101.72        15.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        8.22        14.27        78.67         8.45        15.12        48.46 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       60.72        57.53        53.16        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       11.05         6.21         0.72        10.13        36.99        36.79 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 
       27.25        34.29        30.54        13.94        35.21        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       14.30        80.52         5.62        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       46.03        53.65         3.88        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
       92.81        24.99        40.54       107.21        70.26        31.30 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
       28.67        20.02        27.09        32.71        22.03         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
       23.15        25.41        15.39        18.64        11.28        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       23.08         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
       13.74        20.28        17.72        19.96        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.62        14.66         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        3.25         0.92        15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       40.96        29.92        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-69-7760 TCGA-69-7761 
       14.04        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 
       22.68        13.61         5.42         7.56         6.05        13.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       13.51        14.01        13.45         4.24        19.43         8.42 
TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        6.90        23.38        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
        9.24         1.25        50.33        66.64        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       85.15        49.84        36.66       108.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 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-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
       12.36         5.88        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       19.89        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-86-8585 
       22.82        32.65        31.04        31.20        23.05        11.61 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-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-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        12.23        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
       23.61         1.08        19.00        41.82        18.67        12.39 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       27.29         2.76        19.89        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       61.48        25.48        18.54         0.59        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
        5.39        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       20.58        21.44        19.76        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE 
       34.85        36.76         1.45        21.57        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       32.48        19.00        14.30        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       41.59        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A 
       73.91        71.05        74.33         0.13         1.64         0.49 
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          21.57 
[1] "3.0 - 56.8 (16.1)"  "0.0 - 238.3 (21.6)"
[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      115      129        46        64         67
                vv
clus             STAGE IIIB STAGE IV
  SND1 MUTATED            1        1
  SND1 WILD-TYPE         10       23
D85V3, multiclass
            clus
vv           SND1 MUTATED SND1 WILD-TYPE
  STAGE I               0              4
  STAGE IA              6            115
  STAGE IB              3            129
  STAGE IIA             0             46
  STAGE IIB             2             64
  STAGE IIIA            3             67
  STAGE IIIB            1             10
  STAGE IV              1             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
  SND1 MUTATED     6   7   2   1
  SND1 WILD-TYPE 150 254  41  17
D85V4, multiclass
    clus
vv   SND1 MUTATED SND1 WILD-TYPE
  T1            6            150
  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 298  87    68
D85V5, multiclass
       clus
vv      SND1 MUTATED SND1 WILD-TYPE
  N0              10            298
  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 256 209
[1] "tbl2"
                cls
clus             [,1] [,2]
  SND1 MUTATED      4   12
  SND1 WILD-TYPE  256  209
        clus
vv       SND1 MUTATED SND1 WILD-TYPE
  FEMALE            4            256
  MALE             12            209
[1] 2 2
[1] FALSE
D85V8, binary
                cls
clus               0   1
  SND1 MUTATED    11   3
  SND1 WILD-TYPE 373  52
[1] "tbl2"
                cls
clus             [,1] [,2]
  SND1 MUTATED     11    3
  SND1 WILD-TYPE  373   52
     clus
vv    SND1 MUTATED SND1 WILD-TYPE
  NO            11            373
  YES            3             52
[1] 2 2
[1] FALSE
D85V9, continuous
                vv
clus             LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  SND1 MUTATED                            0                                 5
  SND1 WILD-TYPE                         17                                97
                vv
clus             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  SND1 MUTATED                                                   11
  SND1 WILD-TYPE                                                285
                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                                     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                   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 302  12   4  23
D85V13, multiclass
    clus
vv   SND1 MUTATED SND1 WILD-TYPE
  R0           10            302
  R1            0             12
  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                        29   364
D85V14, multiclass
                                  clus
vv                                 SND1 MUTATED SND1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0              7
  BLACK OR AFRICAN AMERICAN                   1             29
  WHITE                                      14            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"
D85V15, binary
                cls
clus               0   1
  SND1 MUTATED     0  13
  SND1 WILD-TYPE   6 338
[1] "tbl2"
                cls
clus             [,1] [,2]
  SND1 MUTATED      0   13
  SND1 WILD-TYPE    6  338
                        clus
vv                       SND1 MUTATED SND1 WILD-TYPE
  HISPANIC OR LATINO                0              6
  NOT HISPANIC OR LATINO           13            338
[1] 2 2
[1] FALSE

Clustering(86) Variable = C7ORF36 MUTATION ANALYSIS
D86V1, survival
                   sevent
clus2                 0   1
  C7ORF36 MUTATED     3   3
  C7ORF36 WILD-TYPE 295 168
  C7ORF36 MUTATED C7ORF36 WILD-TYPE 
                6               463 
  C7ORF36 MUTATED C7ORF36 WILD-TYPE 
                3               168 
$`C7ORF36 MUTATED`
TCGA-05-4382 TCGA-73-4658 TCGA-49-4486 TCGA-55-8506 TCGA-78-7149 TCGA-78-7536 
       19.96        52.60        76.21         0.36       129.53         8.02 

$`C7ORF36 WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       14.01         9.96         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       13.71        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        10.09        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       24.00         4.96        29.00        22.03         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         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-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       28.11        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       22.26        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        48.46        60.72        57.53        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99        36.79        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       30.54        13.94        35.21        30.58        14.30        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        5.62        42.51        40.73        15.25        46.03        53.65 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
       40.54       107.21        70.26        31.30        28.67        20.02 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       27.09        32.71        22.03         3.91        23.15        25.41 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 
       15.39        18.64        11.28        34.19        17.65        18.44 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 
       19.82        29.23        29.72        15.19        23.08         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       17.79        23.64        15.65        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       17.56        15.72        14.47        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       19.96        26.01        17.10        17.62        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       12.33        20.71        21.40         3.25         0.92        15.81 
TCGA-55-A4DG TCGA-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-64-1679 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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        19.43         8.42         6.90 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       23.38        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
        1.25        50.33        66.64        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       49.84        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        5.69        19.27        20.58        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        9.57       104.19       238.29        88.14        26.53        31.20 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
       53.33        26.01        39.35        10.55       232.18        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59       110.50        93.11        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        38.04        20.55        32.78        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       35.24        37.74         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       22.82        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       14.60        11.61        13.91        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-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-91-6840 
       10.62        41.36         1.97        10.19         2.60        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45        17.46        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       41.82        18.67        12.39        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       42.25        64.60        63.52        61.48        25.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59        15.91        18.67         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.57        18.08        35.47        32.48        19.00        14.30 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        47.08         0.49         0.43        19.82 
TCGA-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             21.47 
[1] "0.4 - 129.5 (36.3)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.2"
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      120      130        46        65         69
                   vv
clus                STAGE IIIB STAGE IV
  C7ORF36 MUTATED            1        0
  C7ORF36 WILD-TYPE         10       24
D86V3, multiclass
            clus
vv           C7ORF36 MUTATED C7ORF36 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 1               120
  STAGE IB                 2               130
  STAGE IIA                0                46
  STAGE IIB                1                65
  STAGE IIIA               1                69
  STAGE IIIB               1                10
  STAGE IV                 0                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
  C7ORF36 MUTATED     1   3   1   1
  C7ORF36 WILD-TYPE 155 258  42  17
D86V4, multiclass
    clus
vv   C7ORF36 MUTATED C7ORF36 WILD-TYPE
  T1               1               155
  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 303  89    71
D86V5, multiclass
       clus
vv      C7ORF36 MUTATED C7ORF36 WILD-TYPE
  N0                  5               303
  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 258 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF36 MUTATED      2    4
  C7ORF36 WILD-TYPE  258  217
        clus
vv       C7ORF36 MUTATED C7ORF36 WILD-TYPE
  FEMALE               2               258
  MALE                 4               217
[1] 2 2
[1] FALSE
D86V8, binary
                   cls
clus                  0   1
  C7ORF36 MUTATED     3   2
  C7ORF36 WILD-TYPE 381  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF36 MUTATED      3    2
  C7ORF36 WILD-TYPE  381   53
     clus
vv    C7ORF36 MUTATED C7ORF36 WILD-TYPE
  NO                3               381
  YES               2                53
[1] 2 2
[1] FALSE
D86V9, continuous
[1] "Remove cluster labels:" "C7ORF36 MUTATED"       
clus
  C7ORF36 MUTATED C7ORF36 WILD-TYPE 
                1               121 
       TCGA-44-6147        TCGA-44-A47F        TCGA-49-6742        TCGA-55-7573 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-55-7725        TCGA-55-7914        TCGA-55-8205        TCGA-55-8511 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-55-8619        TCGA-55-8621        TCGA-55-A491        TCGA-55-A492 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-64-1677        TCGA-73-4662        TCGA-73-7498        TCGA-93-8067 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-MN-A4N1        TCGA-35-4122        TCGA-35-4123        TCGA-35-5375 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-44-3396        TCGA-44-3918        TCGA-44-4112        TCGA-44-6144 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-44-6775        TCGA-44-7660        TCGA-49-4494        TCGA-49-4505 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-49-4506        TCGA-49-4510        TCGA-49-6743        TCGA-49-6744 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-53-7624        TCGA-53-A4EZ        TCGA-55-5899        TCGA-55-7283 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-55-7574        TCGA-55-7910        TCGA-55-7913        TCGA-55-7995 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-55-8089        TCGA-55-8096        TCGA-55-8208        TCGA-55-8507 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-55-8508        TCGA-55-8512        TCGA-55-8513        TCGA-55-8620 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-55-A48Z        TCGA-55-A490        TCGA-55-A494        TCGA-62-8394 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-62-8395        TCGA-62-8397        TCGA-62-8398        TCGA-62-8399 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-62-8402        TCGA-62-A46O        TCGA-62-A46P        TCGA-62-A46R 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-62-A46S        TCGA-62-A46U        TCGA-62-A46V        TCGA-62-A46Y 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-62-A470        TCGA-62-A471        TCGA-62-A472        TCGA-64-1681 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-64-5775        TCGA-64-5778        TCGA-69-7974        TCGA-69-8254 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-71-6725        TCGA-71-8520        TCGA-73-4659        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-73-7499        TCGA-75-5122        TCGA-83-5908        TCGA-86-6562 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-86-6851        TCGA-86-7701        TCGA-86-7711        TCGA-86-7713 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-86-7714        TCGA-86-7953        TCGA-86-7954        TCGA-86-7955 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-86-8054        TCGA-86-8055        TCGA-86-8056        TCGA-86-8073 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-86-8074        TCGA-86-8075        TCGA-86-8076        TCGA-86-8278 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-86-8279        TCGA-86-8280        TCGA-86-8281        TCGA-86-8358 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-86-8359        TCGA-86-8668        TCGA-86-8669        TCGA-86-8671 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-86-A456        TCGA-86-A4JF        TCGA-86-A4P7        TCGA-91-6829 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-91-6849        TCGA-93-7347        TCGA-93-7348        TCGA-93-A4JN 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-93-A4JO        TCGA-95-7567        TCGA-99-7458        TCGA-MN-A4N4 
"C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" "C7ORF36 WILD-TYPE" 
       TCGA-MN-A4N5 
"C7ORF36 WILD-TYPE" 
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  C7ORF36 MUTATED                            0
  C7ORF36 WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  C7ORF36 MUTATED                                   2
  C7ORF36 WILD-TYPE                               100
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  C7ORF36 MUTATED                                                    4
  C7ORF36 WILD-TYPE                                                292
                   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                                        17
  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"
D86V11, continuous
D86V12, continuous
                   vv
clus                 R0  R1  R2  RX
  C7ORF36 MUTATED     6   0   0   0
  C7ORF36 WILD-TYPE 306  12   4  25
D86V13, multiclass
    clus
vv   C7ORF36 MUTATED C7ORF36 WILD-TYPE
  R0               6               306
  R1               0                12
  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                        30   373
D86V14, multiclass
                                  clus
vv                                 C7ORF36 MUTATED C7ORF36 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                30
  WHITE                                          5               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"
D86V15, binary
                   cls
clus                  0   1
  C7ORF36 MUTATED     0   3
  C7ORF36 WILD-TYPE   6 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF36 MUTATED      0    3
  C7ORF36 WILD-TYPE    6  348
                        clus
vv                       C7ORF36 MUTATED C7ORF36 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               3               348
[1] 2 2
[1] FALSE

Clustering(87) Variable = HTRA1 MUTATION ANALYSIS
D87V1, survival
                 sevent
clus2               0   1
  HTRA1 MUTATED     7   3
  HTRA1 WILD-TYPE 291 168
  HTRA1 MUTATED HTRA1 WILD-TYPE 
             10             459 
  HTRA1 MUTATED HTRA1 WILD-TYPE 
              3             168 
$`HTRA1 MUTATED`
TCGA-49-6745 TCGA-05-5425 TCGA-55-8507 TCGA-75-5146 TCGA-78-7156 TCGA-86-8055 
       17.16        29.00        13.74        77.85        32.09         4.08 
TCGA-99-8025 TCGA-MN-A4N4 TCGA-NJ-A4YQ TCGA-O1-A52J 
       34.85        38.63        47.08        59.11 

$`HTRA1 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       16.04        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       14.53        21.44         6.15        19.66        19.73        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       16.93        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       22.65        20.58        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       29.98        12.00        30.02        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       25.02        24.00         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-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         4.37        46.98        44.42        42.77 
TCGA-44-3396 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-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        32.45        61.28        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       55.33        22.26        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       53.16        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 
       34.29        30.54        13.94        35.21        30.58        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       80.52         5.62        42.51        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       53.65         3.88        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 
       24.99        40.54       107.21        70.26        31.30        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       20.02        27.09        32.71        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       25.41        15.39        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.44        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
       15.42        17.56        15.72        14.47         0.36        20.28 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
        1.58        12.33        20.71        21.40         3.25         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       56.81        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-69-7760 TCGA-69-7761 TCGA-69-7763 
       14.73         5.72         4.64         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        13.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
       13.51        14.01        13.45         4.24        19.43         8.42 
TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        6.90        23.38        26.30        15.35         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5147 TCGA-75-6206 
        9.24         1.25        50.33        66.64        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       49.84        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 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-78-7167 TCGA-78-7220 TCGA-78-7535 
        9.57       104.19       238.29        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59       110.50        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 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        11.61        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-91-6840 
       10.62        41.36         1.97        10.19         2.60        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45        17.46        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       41.82        18.67        12.39        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       42.25        64.60        63.52        61.48        25.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59        15.91        18.67         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.84        18.67        24.56        36.76         1.45        21.57 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N5 
       18.08        35.47        32.48        19.00        14.30         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        5.49        41.59        29.46        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        74.33         0.13         1.64 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.49         0.43        19.82 

  HTRA1 MUTATED HTRA1 WILD-TYPE 
           4.08            0.00 
  HTRA1 MUTATED HTRA1 WILD-TYPE 
          77.85          238.29 
  HTRA1 MUTATED HTRA1 WILD-TYPE 
          33.47           21.44 
[1] "4.1 - 77.8 (33.5)"  "0.0 - 238.3 (21.4)"
[1] "hr=" "1.6"
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      117      131        45        65         68
                 vv
clus              STAGE IIIB STAGE IV
  HTRA1 MUTATED            0        1
  HTRA1 WILD-TYPE         11       23
D87V3, multiclass
            clus
vv           HTRA1 MUTATED HTRA1 WILD-TYPE
  STAGE I                0               4
  STAGE IA               4             117
  STAGE IB               1             131
  STAGE IIA              1              45
  STAGE IIB              1              65
  STAGE IIIA             2              68
  STAGE IIIB             0              11
  STAGE IV               1              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
  HTRA1 MUTATED     4   4   1   1
  HTRA1 WILD-TYPE 152 257  42  17
D87V4, multiclass
    clus
vv   HTRA1 MUTATED HTRA1 WILD-TYPE
  T1             4             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
  HTRA1 MUTATED     5   3     2
  HTRA1 WILD-TYPE 303  86    70
D87V5, multiclass
       clus
vv      HTRA1 MUTATED HTRA1 WILD-TYPE
  N0                5             303
  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 257 214
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA1 MUTATED      3    7
  HTRA1 WILD-TYPE  257  214
        clus
vv       HTRA1 MUTATED HTRA1 WILD-TYPE
  FEMALE             3             257
  MALE               7             214
[1] 2 2
[1] FALSE
D87V8, binary
                 cls
clus                0   1
  HTRA1 MUTATED     9   1
  HTRA1 WILD-TYPE 375  54
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA1 MUTATED      9    1
  HTRA1 WILD-TYPE  375   54
     clus
vv    HTRA1 MUTATED HTRA1 WILD-TYPE
  NO              9             375
  YES             1              54
[1] 2 2
[1] FALSE
D87V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  HTRA1 MUTATED                            0                                 2
  HTRA1 WILD-TYPE                         17                               100
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  HTRA1 MUTATED                                                    8
  HTRA1 WILD-TYPE                                                288
                 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                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                              100
  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"
D87V11, continuous
D87V12, continuous
                 vv
clus               R0  R1  R2  RX
  HTRA1 MUTATED     7   0   0   1
  HTRA1 WILD-TYPE 305  12   4  24
D87V13, multiclass
    clus
vv   HTRA1 MUTATED HTRA1 WILD-TYPE
  R0             7             305
  R1             0              12
  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                        29   371
D87V14, multiclass
                                  clus
vv                                 HTRA1 MUTATED HTRA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               7
  BLACK OR AFRICAN AMERICAN                    1              29
  WHITE                                        7             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"
D87V15, binary
                 cls
clus                0   1
  HTRA1 MUTATED     0   6
  HTRA1 WILD-TYPE   6 345
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTRA1 MUTATED      0    6
  HTRA1 WILD-TYPE    6  345
                        clus
vv                       HTRA1 MUTATED HTRA1 WILD-TYPE
  HISPANIC OR LATINO                 0               6
  NOT HISPANIC OR LATINO             6             345
[1] 2 2
[1] FALSE

Clustering(88) Variable = ADAMTS2 MUTATION ANALYSIS
D88V1, survival
                   sevent
clus2                 0   1
  ADAMTS2 MUTATED    30   9
  ADAMTS2 WILD-TYPE 268 162
  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
               39               430 
  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
                9               162 
$`ADAMTS2 MUTATED`
TCGA-05-4382 TCGA-05-4427 TCGA-44-A47F TCGA-55-8207 TCGA-55-A492 TCGA-93-8067 
       19.96        26.01        11.08        32.12        19.59         6.12 
TCGA-97-A4M3 TCGA-J2-8194 TCGA-L9-A444 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       17.75        23.80        10.09        37.02         0.00        24.03 
TCGA-44-4112 TCGA-44-6777 TCGA-50-6593 TCGA-55-6642 TCGA-55-7227 TCGA-55-7281 
       26.56        32.45        11.05        80.52        31.30        28.67 
TCGA-55-7995 TCGA-55-8089 TCGA-55-8506 TCGA-55-8616 TCGA-55-A4DG TCGA-64-1676 
       29.23        23.08         0.36         1.58        19.99        56.81 
TCGA-69-7980 TCGA-75-5146 TCGA-78-7155 TCGA-80-5608 TCGA-83-5908 TCGA-86-7713 
       13.51        77.85        38.50        93.11        27.09        38.04 
TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-A456 TCGA-91-6831 TCGA-95-7039 
       35.24         4.57        24.33        29.46        10.19        41.82 
TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ 
       71.05         0.13        47.08 

$`ADAMTS2 WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4434 
       14.01         9.96         8.02        20.05         9.01        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
       15.02        28.41        35.28        11.64        14.73        26.30 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       38.10        23.93        27.78        86.01        18.31        29.00 
TCGA-44-7671 TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 
       29.23         9.37        46.72        16.04        17.16        11.64 
TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 
       40.60        21.47        41.69        23.05        48.62         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.79         7.99        16.01        23.18        14.53        21.44 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 
        6.15        19.66        19.73        17.98        16.93        19.69 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DF 
       18.15        13.68        16.93        22.65        20.58        20.19 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       20.65        13.87        52.60        82.68        39.09         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
       50.24        10.55        85.32        13.71        16.18         1.45 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       17.29        16.54         2.86        15.68        15.65        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M7 TCGA-J2-8192 
       18.18        17.92        20.19        20.52        20.68        24.30 
TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
        6.35        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       50.07         3.98        45.01        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        24.00         4.96        29.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 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-38-4632 TCGA-38-A44F TCGA-44-2656 
      120.79        37.71        49.05        44.61         4.37        46.98 
TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
       44.42        42.77        37.15        38.24        34.06        33.73 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       21.63        23.18        61.28        16.44        22.72        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
       55.33        22.26        20.52        71.47       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 
       53.16        42.35         3.91        25.55        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        0.72        10.13        36.99        36.79        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 
       30.54        13.94        35.21        30.58        14.30         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
      107.21        70.26        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        3.91        23.15        25.41        15.39        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
       34.19        17.65        18.44        19.82        29.72        15.19 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
       15.42        17.56        15.72        14.47        13.74        20.28 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       12.33        20.71        21.40         3.25         0.92        15.81 
TCGA-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-64-1679 TCGA-64-1681 
       13.61        39.25        40.96        29.92        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-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         4.41        13.41        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       19.43         8.42         6.90        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 
        4.31        30.31         9.24         1.25        50.33        66.64 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
       21.90        39.95       119.51        19.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 
       64.90        22.92         9.57       104.19       238.29        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-86-6562 
       10.55       232.18        39.75        77.59       110.50        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
        5.88        31.13        34.39        20.55        32.78        19.89 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
       37.74         4.08         0.79        22.82        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       31.20        23.05        21.47        14.60        11.61        13.91 
TCGA-86-8669 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-91-6835 
       13.64        26.47        10.62        41.36         1.97         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.18        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       19.00        18.67        12.39        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       42.25        64.60        63.52        61.48        25.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59        15.91        18.67         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.57        18.08        35.47        32.48        19.00        14.30 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP 
       24.36        14.10        19.13        73.91        74.33         1.64 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.49         0.43        19.82        59.11 

  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
             0.00              0.43 
  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
            93.11            238.29 
  ADAMTS2 MUTATED ADAMTS2 WILD-TYPE 
            26.01             21.12 
[1] "0.0 - 93.1 (26.0)"  "0.4 - 238.3 (21.1)"
[1] "hr=" "1.7"
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      108      119        45        60         66
                   vv
clus                STAGE IIIB STAGE IV
  ADAMTS2 MUTATED            1        0
  ADAMTS2 WILD-TYPE         10       24
D88V3, multiclass
            clus
vv           ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                13               108
  STAGE IB                13               119
  STAGE IIA                1                45
  STAGE IIB                6                60
  STAGE IIIA               4                66
  STAGE IIIB               1                10
  STAGE IV                 0                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
  ADAMTS2 MUTATED    15  18   4   2
  ADAMTS2 WILD-TYPE 141 243  39  16
D88V4, multiclass
    clus
vv   ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  T1              15               141
  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 277  85    69
D88V5, multiclass
       clus
vv      ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  N0                 31               277
  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 238 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS2 MUTATED     22   17
  ADAMTS2 WILD-TYPE  238  204
        clus
vv       ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  FEMALE              22               238
  MALE                17               204
[1] 2 2
[1] FALSE
D88V8, binary
                   cls
clus                  0   1
  ADAMTS2 MUTATED    28   5
  ADAMTS2 WILD-TYPE 356  50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS2 MUTATED     28    5
  ADAMTS2 WILD-TYPE  356   50
     clus
vv    ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  NO               28               356
  YES               5                50
[1] 2 2
[1] FALSE
D88V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  ADAMTS2 MUTATED                            1
  ADAMTS2 WILD-TYPE                         16
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  ADAMTS2 MUTATED                                  10
  ADAMTS2 WILD-TYPE                                92
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  ADAMTS2 MUTATED                                                   25
  ADAMTS2 WILD-TYPE                                                271
                   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                                        16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 92
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               271
  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    27   0   0   3
  ADAMTS2 WILD-TYPE 285  12   4  22
D88V13, multiclass
    clus
vv   ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  R0              27               285
  R1               0                12
  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                        29   349
D88V14, multiclass
                                  clus
vv                                 ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 5
  BLACK OR AFRICAN AMERICAN                      1                29
  WHITE                                         29               349
[1] 4 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   6 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS2 MUTATED      0   27
  ADAMTS2 WILD-TYPE    6  324
                        clus
vv                       ADAMTS2 MUTATED ADAMTS2 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO              27               324
[1] 2 2
[1] FALSE

Clustering(89) Variable = TAF1L MUTATION ANALYSIS
D89V1, survival
                 sevent
clus2               0   1
  TAF1L MUTATED    31  17
  TAF1L WILD-TYPE 267 154
  TAF1L MUTATED TAF1L WILD-TYPE 
             48             421 
  TAF1L MUTATED TAF1L WILD-TYPE 
             17             154 
$`TAF1L MUTATED`
TCGA-05-4384 TCGA-05-4396 TCGA-38-4631 TCGA-44-8119 TCGA-55-1592 TCGA-55-8204 
       14.01         9.96        11.64         9.37        23.05        16.93 
TCGA-55-8621 TCGA-55-A4DF TCGA-78-7166 TCGA-91-A4BC TCGA-L9-A444 TCGA-35-4122 
       16.93        20.19         8.48         1.45        10.09         7.40 
TCGA-44-2656 TCGA-44-2657 TCGA-44-5643 TCGA-44-7662 TCGA-44-A479 TCGA-50-5049 
       46.98        44.42        33.30         7.17        15.98       101.72 
TCGA-50-6590 TCGA-50-6593 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-6972 TCGA-55-7281 
       42.35        11.05        30.54        35.21        53.65        28.67 
TCGA-55-7995 TCGA-55-8301 TCGA-64-5778 TCGA-69-7980 TCGA-69-A59K TCGA-78-7145 
       29.23        17.56        42.90        13.51        19.43        27.16 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
      129.53        21.90        39.95        38.50        32.09         5.88 
TCGA-78-7167 TCGA-78-7536 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-A456 
       88.14         8.02        27.09         5.88        31.13        29.46 
TCGA-97-7937 TCGA-99-8032 TCGA-MN-A4N4 TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55R 
       18.54         1.45        38.63        71.05        47.08        19.82 

$`TAF1L WILD-TYPE`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 
       19.96         8.02        20.05         9.01        26.01        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 
       15.02        28.41        35.28        14.73        26.30        38.10 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 
       23.93        27.78        86.01        18.31        29.00        29.23 
TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 
       11.08        46.72        16.04        17.16        11.64        40.60 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 
       21.47        41.69        48.62         5.79         7.79         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 
       16.01        23.18        14.53        21.44         6.15        19.66 
TCGA-55-8091 TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       19.73        17.98        19.69        32.12        18.15        13.68 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       22.65        20.58        19.59        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 
       82.68        39.09        50.24        10.55        85.32        13.71 
TCGA-91-7771 TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 
       16.18         6.12        17.29        16.54         2.86        15.68 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 
       15.65        21.40        18.18        17.92        20.19        20.52 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-MN-A4N1 
       17.75        20.68        24.30        23.80         6.35        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
        5.29        31.23         2.43        10.09        50.07         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
       45.01        37.02         0.00        24.03        47.05        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       26.01        25.02        25.02        24.00         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
       22.03         9.04         2.04         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2665 
      120.79        37.71        49.05        44.61         4.37        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-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7667 
       32.45        61.28        16.44        22.72        19.46        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B 
       18.87        23.64        12.66         8.55        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       12.66        35.54        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-50-5044 
       29.75        55.89        53.29        55.33        22.26        20.52 
TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       71.47        15.72        60.16        47.41        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        9.27        14.27        78.67         8.45        15.12        48.46 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 
       60.72        57.53        53.16         3.91        25.55        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7813 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       34.29        13.94        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 
       42.51        40.73        15.25        46.03         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7227 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       70.26        31.30        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 
        3.91        23.15        25.41        15.39        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
       34.19        17.65        18.44        19.82        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       23.08         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       22.16        15.42        15.72        14.47         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       14.66         1.58        12.33        20.71        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        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-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       29.92        56.81        81.80        38.37        87.98         2.04 
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-69-7760 TCGA-69-7761 TCGA-69-7763 
       14.73         5.72         4.64         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        13.41 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-71-8520 TCGA-73-4659 
       14.01        13.45         4.24         8.42         6.90        23.38 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
       50.33        66.64        77.85        43.82        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 
       36.66       108.66       100.57       163.10         5.69        19.27 
TCGA-78-7148 TCGA-78-7153 TCGA-78-7154 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       20.58       119.51        19.50        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 
      104.19       238.29        26.53        31.20        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-86-6562 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
       93.11        12.36        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        11.61        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
        0.62        28.34        26.50        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
       10.62        41.36         1.97        10.19         2.60        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82        22.45        17.46        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       41.82        18.67        12.39        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 
       42.25        64.60        63.52        61.48        25.48         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       15.91        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       14.30        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-A4AD 
       18.67        24.56        34.85        36.76        21.57        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N5 TCGA-MP-A4SV 
       35.47        32.48        19.00        14.30         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
       41.59        29.46        11.05        24.36        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O 
       73.91        74.33         0.13         1.64         0.49         0.43 
TCGA-O1-A52J 
       59.11 

  TAF1L MUTATED TAF1L WILD-TYPE 
           1.45            0.00 
  TAF1L MUTATED TAF1L WILD-TYPE 
         129.53          238.29 
  TAF1L MUTATED TAF1L WILD-TYPE 
         22.475          21.440 
[1] "1.4 - 129.5 (22.5)" "0.0 - 238.3 (21.4)"
[1] "hr=" "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      106      118        42        62         65
                 vv
clus              STAGE IIIB STAGE IV
  TAF1L MUTATED            3        4
  TAF1L WILD-TYPE          8       20
D89V3, multiclass
            clus
vv           TAF1L MUTATED TAF1L WILD-TYPE
  STAGE I                1               3
  STAGE IA              15             106
  STAGE IB              14             118
  STAGE IIA              4              42
  STAGE IIB              4              62
  STAGE IIIA             5              65
  STAGE IIIB             3               8
  STAGE IV               4              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
  TAF1L MUTATED    17  25   3   5
  TAF1L WILD-TYPE 139 236  40  13
D89V4, multiclass
    clus
vv   TAF1L MUTATED TAF1L WILD-TYPE
  T1            17             139
  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 273  81    66
D89V5, multiclass
       clus
vv      TAF1L MUTATED TAF1L WILD-TYPE
  N0               35             273
  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 239 192
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1L MUTATED     21   29
  TAF1L WILD-TYPE  239  192
        clus
vv       TAF1L MUTATED TAF1L WILD-TYPE
  FEMALE            21             239
  MALE              29             192
[1] 2 2
[1] FALSE
D89V8, binary
                 cls
clus                0   1
  TAF1L MUTATED    38   7
  TAF1L WILD-TYPE 346  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1L MUTATED     38    7
  TAF1L WILD-TYPE  346   48
     clus
vv    TAF1L MUTATED TAF1L WILD-TYPE
  NO             38             346
  YES             7              48
[1] 2 2
[1] FALSE
D89V9, continuous
                 vv
clus              LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  TAF1L MUTATED                            1                                11
  TAF1L WILD-TYPE                         16                                91
                 vv
clus              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  TAF1L MUTATED                                                   32
  TAF1L WILD-TYPE                                                264
                 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                                      16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               91
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             264
  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 282  10   3  21
D89V13, multiclass
    clus
vv   TAF1L MUTATED TAF1L WILD-TYPE
  R0            30             282
  R1             2              10
  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                        26   337
D89V14, multiclass
                                  clus
vv                                 TAF1L MUTATED TAF1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               6
  BLACK OR AFRICAN AMERICAN                    4              26
  WHITE                                       41             337
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V15, binary
                 cls
clus                0   1
  TAF1L MUTATED     1  34
  TAF1L WILD-TYPE   5 317
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF1L MUTATED      1   34
  TAF1L WILD-TYPE    5  317
                        clus
vv                       TAF1L MUTATED TAF1L WILD-TYPE
  HISPANIC OR LATINO                 1               5
  NOT HISPANIC OR LATINO            34             317
[1] 2 2
[1] FALSE

Clustering(90) Variable = PLEKHB2 MUTATION ANALYSIS
D90V1, survival
                   sevent
clus2                 0   1
  PLEKHB2 MUTATED     4   2
  PLEKHB2 WILD-TYPE 294 169
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                6               463 
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                2               169 
$`PLEKHB2 MUTATED`
TCGA-55-A4DF TCGA-44-7662 TCGA-49-6767 TCGA-50-5941 TCGA-MP-A4SV TCGA-NJ-A55R 
       20.19         7.17        22.26        48.46        86.14        19.82 

$`PLEKHB2 WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       18.31        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16        11.64        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       23.05        48.62         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-64-1677 TCGA-67-6217 
       16.93        22.65        20.58        19.59        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       23.80         6.35        10.09        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        2.43        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       29.98        12.00        30.02        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       25.02        24.00         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       37.71        49.05        44.61         4.37        46.98        44.42 
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-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        32.45        61.28        16.44        22.72 
TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
       19.46        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       55.33        20.52        71.47       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
        8.45        15.12        60.72        57.53        53.16        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
        3.91        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99        36.79        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       13.94        35.21        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
      107.21        70.26        31.30        28.67        20.02        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 
       32.71        22.03         3.91        23.15        25.41        15.39 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       18.64        11.28        34.19        17.65        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       29.23        29.72        15.19        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       15.72        14.47         0.36        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       19.96        26.01        17.10        17.62        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       12.33        20.71        21.40         3.25         0.92        15.81 
TCGA-55-A4DG TCGA-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-64-1679 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-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 
       14.01        13.45         4.24        19.43         8.42         6.90 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       23.38        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
        1.25        50.33        66.64        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       49.84        36.66       108.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        5.69        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
       22.92         9.57       104.19       238.29        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
      232.18        39.75        77.59       110.50        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       12.36         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       32.78        19.89        35.24        37.74         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
       24.33         0.79        22.82        32.65        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       23.05        21.47        14.60        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        28.34        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
        1.08        19.00        41.82        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       25.48        18.54         0.59        15.91        18.67         5.39 
TCGA-97-8175 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-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       36.76         1.45        21.57        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY 
       19.00        14.30        38.63         2.76        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE 
       37.35        86.04        58.85         5.49        41.59        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-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 
       74.33         0.13         1.64        47.08         0.49         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 
           21.225            21.470 
[1] "7.2 - 86.1 (21.2)"  "0.0 - 238.3 (21.5)"
[1] "hr=" "1.3"
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      119      130        46        65         69
                   vv
clus                STAGE IIIB STAGE IV
  PLEKHB2 MUTATED            0        0
  PLEKHB2 WILD-TYPE         11       24
D90V3, multiclass
            clus
vv           PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 2               119
  STAGE IB                 2               130
  STAGE IIA                0                46
  STAGE IIB                1                65
  STAGE IIIA               1                69
  STAGE IIIB               0                11
  STAGE IV                 0                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
  PLEKHB2 MUTATED     2   3   1   0
  PLEKHB2 WILD-TYPE 154 258  42  18
D90V4, multiclass
    clus
vv   PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  T1               2               154
  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 303  89    71
D90V5, multiclass
       clus
vv      PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  N0                  5               303
  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 258 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      2    4
  PLEKHB2 WILD-TYPE  258  217
        clus
vv       PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  FEMALE               2               258
  MALE                 4               217
[1] 2 2
[1] FALSE
D90V8, binary
                   cls
clus                  0   1
  PLEKHB2 MUTATED     5   0
  PLEKHB2 WILD-TYPE 379  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      5    0
  PLEKHB2 WILD-TYPE  379   55
     clus
vv    PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  NO                5               379
  YES               0                55
[1] 2 2
[1] FALSE
D90V9, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  PLEKHB2 MUTATED                            0
  PLEKHB2 WILD-TYPE                         17
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  PLEKHB2 MUTATED                                   0
  PLEKHB2 WILD-TYPE                               102
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  PLEKHB2 MUTATED                                                    6
  PLEKHB2 WILD-TYPE                                                290
                   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                                        17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                102
  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"
D90V11, continuous
D90V12, continuous
[1] "Remove cluster labels:" "PLEKHB2 MUTATED"       
clus
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                2               256 
       TCGA-05-4384        TCGA-05-4396        TCGA-05-4405        TCGA-05-4410 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-05-4427        TCGA-05-5420        TCGA-38-7271        TCGA-44-6147 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-44-6776        TCGA-44-7661        TCGA-44-7670        TCGA-44-8119 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-44-A47F        TCGA-55-1592        TCGA-55-1595        TCGA-55-7724 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-7725        TCGA-55-7726        TCGA-55-7914        TCGA-55-8205 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-8511        TCGA-55-8621        TCGA-55-A48X        TCGA-55-A491 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-A492        TCGA-64-1677        TCGA-73-4662        TCGA-73-7498 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-78-7166        TCGA-78-7633        TCGA-78-8660        TCGA-80-5607 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-91-6836        TCGA-91-A4BC        TCGA-93-8067        TCGA-93-A4JQ 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-95-7043        TCGA-95-7562        TCGA-95-7947        TCGA-95-7948 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-95-A4VK        TCGA-95-A4VN        TCGA-97-8172        TCGA-97-A4LX 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-97-A4M2        TCGA-97-A4M3        TCGA-97-A4M7        TCGA-J2-8194 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-L9-A443        TCGA-L9-A444        TCGA-MN-A4N1        TCGA-MP-A4T8 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-MP-A4TA        TCGA-MP-A4TC        TCGA-05-4390        TCGA-05-4415 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-05-4417        TCGA-05-4424        TCGA-05-4433        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-A44F 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-44-2656        TCGA-44-2657        TCGA-44-3396        TCGA-44-3398 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-44-3918        TCGA-44-4112        TCGA-44-5644        TCGA-44-5645 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-44-6144        TCGA-44-6145        TCGA-44-6148        TCGA-44-6774 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-44-6775        TCGA-44-6777        TCGA-44-6778        TCGA-44-6779 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-44-7659        TCGA-44-7660        TCGA-44-7667        TCGA-44-7669 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-44-7672        TCGA-44-8117        TCGA-44-8120        TCGA-44-A479 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-44-A47A        TCGA-44-A47B        TCGA-44-A47G        TCGA-44-A4SS 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-44-A4SU        TCGA-49-4486        TCGA-49-4494        TCGA-49-4505 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-53-7624        TCGA-53-7626        TCGA-53-7813        TCGA-53-A4EZ 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-5899        TCGA-55-6642        TCGA-55-6712        TCGA-55-6971 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-7227        TCGA-55-7283        TCGA-55-7570        TCGA-55-7574 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-7576        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-55-7913        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-55-8299 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-8301        TCGA-55-8302        TCGA-55-8506        TCGA-55-8507 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-8512        TCGA-55-8514        TCGA-55-8615        TCGA-55-8620 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-A48Y        TCGA-55-A48Z        TCGA-55-A490        TCGA-55-A493 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-55-A494        TCGA-62-8398        TCGA-64-1681        TCGA-64-5774 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-64-5775        TCGA-64-5778        TCGA-64-5779        TCGA-64-5781 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-69-7761        TCGA-69-7763        TCGA-69-7764        TCGA-69-7765 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-69-7974        TCGA-69-7979        TCGA-69-8253        TCGA-69-8255 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-69-A59K        TCGA-73-4659        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-75-6214 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-75-7025        TCGA-75-7027        TCGA-75-7031        TCGA-78-7145 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-78-7146        TCGA-78-7147        TCGA-78-7148        TCGA-78-7149 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-78-7150        TCGA-78-7152        TCGA-78-7153        TCGA-78-7154 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-78-7155        TCGA-78-7156        TCGA-78-7158        TCGA-78-7159 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-78-7160        TCGA-78-7161        TCGA-78-7162        TCGA-78-7163 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-78-7167        TCGA-78-7220        TCGA-78-7535        TCGA-78-7536 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-78-7537        TCGA-78-7539        TCGA-78-7542        TCGA-78-8640 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-78-8648        TCGA-78-8655        TCGA-78-8662        TCGA-80-5608 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-83-5908        TCGA-86-6851        TCGA-86-7711        TCGA-86-7714 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-86-7954        TCGA-86-8054        TCGA-86-8055        TCGA-86-8056 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-86-8073        TCGA-86-8074        TCGA-86-8281        TCGA-86-8358 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-86-8359        TCGA-86-8669        TCGA-86-8673        TCGA-86-8674 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-86-A456        TCGA-91-6829        TCGA-91-6830        TCGA-91-6840 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-91-6849        TCGA-91-8499        TCGA-93-7347        TCGA-93-7348 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-93-A4JN        TCGA-93-A4JO        TCGA-95-7567        TCGA-95-7944 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-95-A4VP        TCGA-97-7546        TCGA-97-7553        TCGA-97-7554 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-97-7941        TCGA-97-8171        TCGA-97-8174        TCGA-97-8176 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-97-8179        TCGA-97-A4M0        TCGA-97-A4M1        TCGA-97-A4M5 
"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-A4AD        TCGA-J2-A4AG        TCGA-L4-A4E5        TCGA-L4-A4E6 
"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-A4T9        TCGA-MP-A4TE 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-MP-A4TF        TCGA-MP-A4TH        TCGA-MP-A4TI        TCGA-MP-A4TK 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-MP-A5C7        TCGA-NJ-A4YG        TCGA-NJ-A4YI        TCGA-O1-A52J 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
                   vv
clus                 R0  R1  R2  RX
  PLEKHB2 MUTATED     3   0   0   0
  PLEKHB2 WILD-TYPE 309  12   4  25
D90V13, multiclass
    clus
vv   PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  R0               3               309
  R1               0                12
  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                        30   373
D90V14, multiclass
                                  clus
vv                                 PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 7
  BLACK OR AFRICAN AMERICAN                      0                30
  WHITE                                          5               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"
D90V15, binary
                   cls
clus                  0   1
  PLEKHB2 MUTATED     0   3
  PLEKHB2 WILD-TYPE   6 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      0    3
  PLEKHB2 WILD-TYPE    6  348
                        clus
vv                       PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  HISPANIC OR LATINO                   0                 6
  NOT HISPANIC OR LATINO               3               348
[1] 2 2
[1] FALSE
