[1] "ofn"        "-oTDLBC-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/DLBC-TP/19775131/DLBC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/19899504/transformed.cor.cli.txt"

nPatients in clinical file=47, in cluster file=41, common to both=40
[1] "Reduce the number of clustering variables from 110 to 92."
[1] 92 40
[1] "MYD88 MUTATION ANALYSIS"
[1] 3
  MYD88 MUTATED MYD88 WILD-TYPE 
              3              37 
  MYD88 MUTATED MYD88 WILD-TYPE 
              3              37 
[1] "FRG1 MUTATION ANALYSIS"
[1] 3
  FRG1 MUTATED FRG1 WILD-TYPE 
             8             32 
  FRG1 MUTATED FRG1 WILD-TYPE 
             8             32 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            14             26 
  MLL2 MUTATED MLL2 WILD-TYPE 
            14             26 
[1] "TPPP MUTATION ANALYSIS"
[1] 3
  TPPP MUTATED TPPP WILD-TYPE 
             5             35 
  TPPP MUTATED TPPP WILD-TYPE 
             5             35 
[1] "CHIT1 MUTATION ANALYSIS"
[1] 3
  CHIT1 MUTATED CHIT1 WILD-TYPE 
              6              34 
  CHIT1 MUTATED CHIT1 WILD-TYPE 
              6              34 
[1] "B2M MUTATION ANALYSIS"
[1] 3
  B2M MUTATED B2M WILD-TYPE 
            8            32 
  B2M MUTATED B2M WILD-TYPE 
            8            32 
[1] "TPTE2 MUTATION ANALYSIS"
[1] 3
  TPTE2 MUTATED TPTE2 WILD-TYPE 
             11              29 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
             11              29 
[1] "RHPN2 MUTATION ANALYSIS"
[1] 3
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              6              34 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              6              34 
[1] "FOXD4L1 MUTATION ANALYSIS"
[1] 3
  FOXD4L1 MUTATED FOXD4L1 WILD-TYPE 
                7                33 
  FOXD4L1 MUTATED FOXD4L1 WILD-TYPE 
                7                33 
[1] "DND1 MUTATION ANALYSIS"
[1] 3
  DND1 MUTATED DND1 WILD-TYPE 
             4             36 
  DND1 MUTATED DND1 WILD-TYPE 
             4             36 
[1] "ATXN1 MUTATION ANALYSIS"
[1] 3
  ATXN1 MUTATED ATXN1 WILD-TYPE 
              7              33 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
              7              33 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
             6             34 
  TP53 MUTATED TP53 WILD-TYPE 
             6             34 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
             10              30 
  CDC27 MUTATED CDC27 WILD-TYPE 
             10              30 
[1] "EPB41L4A MUTATION ANALYSIS"
[1] 3
  EPB41L4A MUTATED EPB41L4A WILD-TYPE 
                 4                 36 
  EPB41L4A MUTATED EPB41L4A WILD-TYPE 
                 4                 36 
[1] "NOTCH2NL MUTATION ANALYSIS"
[1] 3
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 4                 36 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 4                 36 
[1] "KRT3 MUTATION ANALYSIS"
[1] 3
  KRT3 MUTATED KRT3 WILD-TYPE 
             4             36 
  KRT3 MUTATED KRT3 WILD-TYPE 
             4             36 
[1] "OR1S2 MUTATION ANALYSIS"
[1] 3
  OR1S2 MUTATED OR1S2 WILD-TYPE 
             10              30 
  OR1S2 MUTATED OR1S2 WILD-TYPE 
             10              30 
[1] "RGPD5 MUTATION ANALYSIS"
[1] 3
  RGPD5 MUTATED RGPD5 WILD-TYPE 
              5              35 
  RGPD5 MUTATED RGPD5 WILD-TYPE 
              5              35 
[1] "TNFAIP3 MUTATION ANALYSIS"
[1] 3
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
                6                34 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
                6                34 
[1] "RBMXL1 MUTATION ANALYSIS"
[1] 3
  RBMXL1 MUTATED RBMXL1 WILD-TYPE 
               4               36 
  RBMXL1 MUTATED RBMXL1 WILD-TYPE 
               4               36 
[1] "CCDC66 MUTATION ANALYSIS"
[1] 3
  CCDC66 MUTATED CCDC66 WILD-TYPE 
               4               36 
  CCDC66 MUTATED CCDC66 WILD-TYPE 
               4               36 
[1] "NOTCH2 MUTATION ANALYSIS"
[1] 3
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
               7               33 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
               7               33 
[1] "PCMTD1 MUTATION ANALYSIS"
[1] 3
  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
               6               34 
  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
               6               34 
[1] "FAM120B MUTATION ANALYSIS"
[1] 3
  FAM120B MUTATED FAM120B WILD-TYPE 
                5                35 
  FAM120B MUTATED FAM120B WILD-TYPE 
                5                35 
[1] "SMARCA2 MUTATION ANALYSIS"
[1] 3
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
                4                36 
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
                4                36 
[1] "C11ORF40 MUTATION ANALYSIS"
[1] 3
  C11ORF40 MUTATED C11ORF40 WILD-TYPE 
                 4                 36 
  C11ORF40 MUTATED C11ORF40 WILD-TYPE 
                 4                 36 
[1] "ZSCAN5A MUTATION ANALYSIS"
[1] 3
  ZSCAN5A MUTATED ZSCAN5A WILD-TYPE 
                3                37 
  ZSCAN5A MUTATED ZSCAN5A WILD-TYPE 
                3                37 
[1] "KRTAP4-5 MUTATION ANALYSIS"
[1] 3
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 4                 36 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 4                 36 
[1] "DEFA1 MUTATION ANALYSIS"
[1] 3
  DEFA1 MUTATED DEFA1 WILD-TYPE 
              4              36 
  DEFA1 MUTATED DEFA1 WILD-TYPE 
              4              36 
[1] "SIRPA MUTATION ANALYSIS"
[1] 3
  SIRPA MUTATED SIRPA WILD-TYPE 
              5              35 
  SIRPA MUTATED SIRPA WILD-TYPE 
              5              35 
[1] "TMPRSS13 MUTATION ANALYSIS"
[1] 3
  TMPRSS13 MUTATED TMPRSS13 WILD-TYPE 
                 3                 37 
  TMPRSS13 MUTATED TMPRSS13 WILD-TYPE 
                 3                 37 
[1] "CYP2A6 MUTATION ANALYSIS"
[1] 3
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
               4               36 
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
               4               36 
[1] "AR MUTATION ANALYSIS"
[1] 3
  AR MUTATED AR WILD-TYPE 
           7           33 
  AR MUTATED AR WILD-TYPE 
           7           33 
[1] "ARHGEF5 MUTATION ANALYSIS"
[1] 3
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                3                37 
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                3                37 
[1] "RNF39 MUTATION ANALYSIS"
[1] 3
  RNF39 MUTATED RNF39 WILD-TYPE 
              3              37 
  RNF39 MUTATED RNF39 WILD-TYPE 
              3              37 
[1] "ABCA1 MUTATION ANALYSIS"
[1] 3
  ABCA1 MUTATED ABCA1 WILD-TYPE 
              5              35 
  ABCA1 MUTATED ABCA1 WILD-TYPE 
              5              35 
[1] "CS MUTATION ANALYSIS"
[1] 3
  CS MUTATED CS WILD-TYPE 
           3           37 
  CS MUTATED CS WILD-TYPE 
           3           37 
[1] "IFITM3 MUTATION ANALYSIS"
[1] 3
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               4               36 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               4               36 
[1] "RANBP2 MUTATION ANALYSIS"
[1] 3
  RANBP2 MUTATED RANBP2 WILD-TYPE 
               5               35 
  RANBP2 MUTATED RANBP2 WILD-TYPE 
               5               35 
[1] "KLHL6 MUTATION ANALYSIS"
[1] 3
  KLHL6 MUTATED KLHL6 WILD-TYPE 
              6              34 
  KLHL6 MUTATED KLHL6 WILD-TYPE 
              6              34 
[1] "ZNF814 MUTATION ANALYSIS"
[1] 3
  ZNF814 MUTATED ZNF814 WILD-TYPE 
              10               30 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
              10               30 
[1] "CYP4A11 MUTATION ANALYSIS"
[1] 3
  CYP4A11 MUTATED CYP4A11 WILD-TYPE 
                4                36 
  CYP4A11 MUTATED CYP4A11 WILD-TYPE 
                4                36 
[1] "PIM1 MUTATION ANALYSIS"
[1] 3
  PIM1 MUTATED PIM1 WILD-TYPE 
             8             32 
  PIM1 MUTATED PIM1 WILD-TYPE 
             8             32 
[1] "POTEE MUTATION ANALYSIS"
[1] 3
  POTEE MUTATED POTEE WILD-TYPE 
              7              33 
  POTEE MUTATED POTEE WILD-TYPE 
              7              33 
[1] "OR52E6 MUTATION ANALYSIS"
[1] 3
  OR52E6 MUTATED OR52E6 WILD-TYPE 
               3               37 
  OR52E6 MUTATED OR52E6 WILD-TYPE 
               3               37 
[1] "NBPF10 MUTATION ANALYSIS"
[1] 3
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               8               32 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               8               32 
[1] "PRB2 MUTATION ANALYSIS"
[1] 3
  PRB2 MUTATED PRB2 WILD-TYPE 
             8             32 
  PRB2 MUTATED PRB2 WILD-TYPE 
             8             32 
[1] "MUC6 MUTATION ANALYSIS"
[1] 3
  MUC6 MUTATED MUC6 WILD-TYPE 
            21             19 
  MUC6 MUTATED MUC6 WILD-TYPE 
            21             19 
[1] "SALL1 MUTATION ANALYSIS"
[1] 3
  SALL1 MUTATED SALL1 WILD-TYPE 
              5              35 
  SALL1 MUTATED SALL1 WILD-TYPE 
              5              35 
[1] "PAK2 MUTATION ANALYSIS"
[1] 3
  PAK2 MUTATED PAK2 WILD-TYPE 
             7             33 
  PAK2 MUTATED PAK2 WILD-TYPE 
             7             33 
[1] "FLG MUTATION ANALYSIS"
[1] 3
  FLG MUTATED FLG WILD-TYPE 
           17            23 
  FLG MUTATED FLG WILD-TYPE 
           17            23 
[1] "MUC17 MUTATION ANALYSIS"
[1] 3
  MUC17 MUTATED MUC17 WILD-TYPE 
             12              28 
  MUC17 MUTATED MUC17 WILD-TYPE 
             12              28 
[1] "OR2T4 MUTATION ANALYSIS"
[1] 3
  OR2T4 MUTATED OR2T4 WILD-TYPE 
              8              32 
  OR2T4 MUTATED OR2T4 WILD-TYPE 
              8              32 
[1] "AMAC1L3 MUTATION ANALYSIS"
[1] 3
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                5                35 
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                5                35 
[1] "APOB MUTATION ANALYSIS"
[1] 3
  APOB MUTATED APOB WILD-TYPE 
             3             37 
  APOB MUTATED APOB WILD-TYPE 
             3             37 
[1] "KRTAP4-7 MUTATION ANALYSIS"
[1] 3
  KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE 
                 8                 32 
  KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE 
                 8                 32 
[1] "MUC16 MUTATION ANALYSIS"
[1] 3
  MUC16 MUTATED MUC16 WILD-TYPE 
             12              28 
  MUC16 MUTATED MUC16 WILD-TYPE 
             12              28 
[1] "NEFH MUTATION ANALYSIS"
[1] 3
  NEFH MUTATED NEFH WILD-TYPE 
             6             34 
  NEFH MUTATED NEFH WILD-TYPE 
             6             34 
[1] "KCNN3 MUTATION ANALYSIS"
[1] 3
  KCNN3 MUTATED KCNN3 WILD-TYPE 
              7              33 
  KCNN3 MUTATED KCNN3 WILD-TYPE 
              7              33 
[1] "RNASEH2B MUTATION ANALYSIS"
[1] 3
  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
                 3                 37 
  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
                 3                 37 
[1] "OTOP1 MUTATION ANALYSIS"
[1] 3
  OTOP1 MUTATED OTOP1 WILD-TYPE 
              4              36 
  OTOP1 MUTATED OTOP1 WILD-TYPE 
              4              36 
[1] "AATK MUTATION ANALYSIS"
[1] 3
  AATK MUTATED AATK WILD-TYPE 
             3             37 
  AATK MUTATED AATK WILD-TYPE 
             3             37 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               35 
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               35 
[1] "GUCA1C MUTATION ANALYSIS"
[1] 3
  GUCA1C MUTATED GUCA1C WILD-TYPE 
               3               37 
  GUCA1C MUTATED GUCA1C WILD-TYPE 
               3               37 
[1] "TRIM48 MUTATION ANALYSIS"
[1] 3
  TRIM48 MUTATED TRIM48 WILD-TYPE 
               8               32 
  TRIM48 MUTATED TRIM48 WILD-TYPE 
               8               32 
[1] "CSGALNACT2 MUTATION ANALYSIS"
[1] 3
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   5                   35 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   5                   35 
[1] "CRIPAK MUTATION ANALYSIS"
[1] 3
  CRIPAK MUTATED CRIPAK WILD-TYPE 
               6               34 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
               6               34 
[1] "DHRS4 MUTATION ANALYSIS"
[1] 3
  DHRS4 MUTATED DHRS4 WILD-TYPE 
              4              36 
  DHRS4 MUTATED DHRS4 WILD-TYPE 
              4              36 
[1] "FAM21A MUTATION ANALYSIS"
[1] 3
  FAM21A MUTATED FAM21A WILD-TYPE 
               4               36 
  FAM21A MUTATED FAM21A WILD-TYPE 
               4               36 
[1] "KIAA1529 MUTATION ANALYSIS"
[1] 3
  KIAA1529 MUTATED KIAA1529 WILD-TYPE 
                 4                 36 
  KIAA1529 MUTATED KIAA1529 WILD-TYPE 
                 4                 36 
[1] "OR2M5 MUTATION ANALYSIS"
[1] 3
  OR2M5 MUTATED OR2M5 WILD-TYPE 
              4              36 
  OR2M5 MUTATED OR2M5 WILD-TYPE 
              4              36 
[1] "KRT6A MUTATION ANALYSIS"
[1] 3
  KRT6A MUTATED KRT6A WILD-TYPE 
              4              36 
  KRT6A MUTATED KRT6A WILD-TYPE 
              4              36 
[1] "CYP2F1 MUTATION ANALYSIS"
[1] 3
  CYP2F1 MUTATED CYP2F1 WILD-TYPE 
               4               36 
  CYP2F1 MUTATED CYP2F1 WILD-TYPE 
               4               36 
[1] "FCGBP MUTATION ANALYSIS"
[1] 3
  FCGBP MUTATED FCGBP WILD-TYPE 
              5              35 
  FCGBP MUTATED FCGBP WILD-TYPE 
              5              35 
[1] "ZNF493 MUTATION ANALYSIS"
[1] 3
  ZNF493 MUTATED ZNF493 WILD-TYPE 
               4               36 
  ZNF493 MUTATED ZNF493 WILD-TYPE 
               4               36 
[1] "HLA-B MUTATION ANALYSIS"
[1] 3
  HLA-B MUTATED HLA-B WILD-TYPE 
              6              34 
  HLA-B MUTATED HLA-B WILD-TYPE 
              6              34 
[1] "FCRLA MUTATION ANALYSIS"
[1] 3
  FCRLA MUTATED FCRLA WILD-TYPE 
              3              37 
  FCRLA MUTATED FCRLA WILD-TYPE 
              3              37 
[1] "KLRC2 MUTATION ANALYSIS"
[1] 3
  KLRC2 MUTATED KLRC2 WILD-TYPE 
              5              35 
  KLRC2 MUTATED KLRC2 WILD-TYPE 
              5              35 
[1] "CD79B MUTATION ANALYSIS"
[1] 3
  CD79B MUTATED CD79B WILD-TYPE 
              5              35 
  CD79B MUTATED CD79B WILD-TYPE 
              5              35 
[1] "TMSB4X MUTATION ANALYSIS"
[1] 3
  TMSB4X MUTATED TMSB4X WILD-TYPE 
               5               35 
  TMSB4X MUTATED TMSB4X WILD-TYPE 
               5               35 
[1] "PRB1 MUTATION ANALYSIS"
[1] 3
  PRB1 MUTATED PRB1 WILD-TYPE 
             5             35 
  PRB1 MUTATED PRB1 WILD-TYPE 
             5             35 
[1] "PCDHA7 MUTATION ANALYSIS"
[1] 3
  PCDHA7 MUTATED PCDHA7 WILD-TYPE 
               4               36 
  PCDHA7 MUTATED PCDHA7 WILD-TYPE 
               4               36 
[1] "OR5H14 MUTATION ANALYSIS"
[1] 3
  OR5H14 MUTATED OR5H14 WILD-TYPE 
               3               37 
  OR5H14 MUTATED OR5H14 WILD-TYPE 
               3               37 
[1] "PER3 MUTATION ANALYSIS"
[1] 3
  PER3 MUTATED PER3 WILD-TYPE 
             4             36 
  PER3 MUTATED PER3 WILD-TYPE 
             4             36 
[1] "PABPC1 MUTATION ANALYSIS"
[1] 3
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               7               33 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               7               33 
[1] "ITGA6 MUTATION ANALYSIS"
[1] 3
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              3              37 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              3              37 
[1] "IGSF3 MUTATION ANALYSIS"
[1] 3
  IGSF3 MUTATED IGSF3 WILD-TYPE 
              6              34 
  IGSF3 MUTATED IGSF3 WILD-TYPE 
              6              34 
[1] "KRTAP1-1 MUTATION ANALYSIS"
[1] 3
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
                 3                 37 
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
                 3                 37 
[1] "C15ORF39 MUTATION ANALYSIS"
[1] 3
  C15ORF39 MUTATED C15ORF39 WILD-TYPE 
                 3                 37 
  C15ORF39 MUTATED C15ORF39 WILD-TYPE 
                 3                 37 
[1] "ZNF880 MUTATION ANALYSIS"
[1] 3
  ZNF880 MUTATED ZNF880 WILD-TYPE 
               8               32 
  ZNF880 MUTATED ZNF880 WILD-TYPE 
               8               32 
[1] "NBPF15 MUTATION ANALYSIS"
[1] 3
  NBPF15 MUTATED NBPF15 WILD-TYPE 
               4               36 
  NBPF15 MUTATED NBPF15 WILD-TYPE 
               4               36 
[1] "SLC22A16 MUTATION ANALYSIS"
[1] 3
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                 3                 37 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                 3                 37 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "PATHOLOGIC_STAGE"                    
 [6] "PATHOLOGY_T_STAGE"                   
 [7] "PATHOLOGY_N_STAGE"                   
 [8] "PATHOLOGY_M_STAGE"                   
 [9] "GENDER"                              
[10] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[11] "RADIATION_THERAPY"                   
[12] "HISTOLOGICAL_TYPE"                   
[13] "RACE"                                
[14] "ETHNICITY"                           

Input Data has 14 rows and 40 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=6,	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=36,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PATHOLOGIC_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'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] "****** SUMMARY ***** "
Output Data has 40 columns, 1 survival variables, and 6 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"    "GENDER"            "RADIATION_THERAPY"
[4] "HISTOLOGICAL_TYPE" "RACE"              "ETHNICITY"        
YEARS_TO_BIRTH, nv=31, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MYD88 MUTATION ANALYSIS
D1V1, survival
                 sevent
clus2              0  1
  MYD88 MUTATED    2  1
  MYD88 WILD-TYPE 32  5
  MYD88 MUTATED MYD88 WILD-TYPE 
              3              37 
  MYD88 MUTATED MYD88 WILD-TYPE 
              1               5 
$`MYD88 MUTATED`
TCGA-FF-A7CR TCGA-FF-A7CX TCGA-RQ-A6JB 
       10.29        12.66         0.03 

$`MYD88 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CW 
       24.69         4.14        27.35        22.32         9.80        26.01 
TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
       31.96        41.16        98.07        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       57.17        32.28        38.24       128.12        24.00        53.16 
TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N 
       45.14       109.58        25.15       111.58        12.85        25.91 
TCGA-RQ-AAAT 
        0.56 

  MYD88 MUTATED MYD88 WILD-TYPE 
           0.03            0.56 
  MYD88 MUTATED MYD88 WILD-TYPE 
          12.66          128.12 
  MYD88 MUTATED MYD88 WILD-TYPE 
          10.29           26.01 
[1] "0.0 - 12.7 (10.3)"  "0.6 - 128.1 (26.0)"
[1] "hr=" "8.1"
D1V2, continuous
D1V3, binary
                 cls
clus               0  1
  MYD88 MUTATED    1  2
  MYD88 WILD-TYPE 23 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYD88 MUTATED      1    2
  MYD88 WILD-TYPE   23   14
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  FEMALE             1              23
  MALE               2              14
[1] 2 2
[1] FALSE
D1V4, binary
                 cls
clus               0  1
  MYD88 MUTATED    2  0
  MYD88 WILD-TYPE 31  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYD88 MUTATED      2    0
  MYD88 WILD-TYPE   31    6
     clus
vv    MYD88 MUTATED MYD88 WILD-TYPE
  NO              2              31
  YES             0               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  MYD88 MUTATED                                                                                   2
  MYD88 WILD-TYPE                                                                                31
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  MYD88 MUTATED                          1                                  0
  MYD88 WILD-TYPE                        2                                  4
D1V5, multiclass
                                                                                   clus
vv                                                                                  MYD88 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             2
  PRIMARY DLBCL OF THE CNS                                                                      1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  MYD88 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              31
  PRIMARY DLBCL OF THE CNS                                                                        2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MYD88 MUTATED       2                         0     1
  MYD88 WILD-TYPE    16                         1    20
D1V6, multiclass
                           clus
vv                          MYD88 MUTATED MYD88 WILD-TYPE
  ASIAN                                 2              16
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 1              20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                 cls
clus               0  1
  MYD88 MUTATED    0  3
  MYD88 WILD-TYPE 12 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYD88 MUTATED      0    3
  MYD88 WILD-TYPE   12   25
                        clus
vv                       MYD88 MUTATED MYD88 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             3              25
[1] 2 2
[1] FALSE

Clustering(2) Variable = FRG1 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2             0  1
  FRG1 MUTATED    7  1
  FRG1 WILD-TYPE 27  5
  FRG1 MUTATED FRG1 WILD-TYPE 
             8             32 
  FRG1 MUTATED FRG1 WILD-TYPE 
             1              5 
$`FRG1 MUTATED`
TCGA-FA-8693 TCGA-FA-A6HN TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8061 
        4.34         1.91        18.18        35.54        31.10        27.35 
TCGA-GR-7353 TCGA-GR-A4D5 
       98.07        42.71 

$`FRG1 WILD-TYPE`
TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34        23.28        24.62        23.64         8.15        14.04 
TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       31.73        24.69         4.14        22.32         9.80        10.29 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-A4D4 TCGA-GR-A4D6 
       26.01        12.66        31.96        41.16        51.98        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       57.17        32.28        38.24       128.12        24.00        53.16 
TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N 
       45.14       109.58        25.15       111.58        12.85        25.91 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  FRG1 MUTATED FRG1 WILD-TYPE 
          1.91           0.03 
  FRG1 MUTATED FRG1 WILD-TYPE 
         98.07         128.12 
  FRG1 MUTATED FRG1 WILD-TYPE 
        29.225         24.920 
[1] "1.9 - 98.1 (29.2)"  "0.0 - 128.1 (24.9)"
[1] "hr=" "1.2"
D2V2, continuous
D2V3, binary
                cls
clus              0  1
  FRG1 MUTATED    4  4
  FRG1 WILD-TYPE 20 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRG1 MUTATED      4    4
  FRG1 WILD-TYPE   20   12
        clus
vv       FRG1 MUTATED FRG1 WILD-TYPE
  FEMALE            4             20
  MALE              4             12
[1] 2 2
[1] FALSE
D2V4, binary
                cls
clus              0  1
  FRG1 MUTATED    8  0
  FRG1 WILD-TYPE 25  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRG1 MUTATED      8    0
  FRG1 WILD-TYPE   25    6
     clus
vv    FRG1 MUTATED FRG1 WILD-TYPE
  NO             8             25
  YES            0              6
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  FRG1 MUTATED                                                                                   7
  FRG1 WILD-TYPE                                                                                26
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  FRG1 MUTATED                          0                                  1
  FRG1 WILD-TYPE                        3                                  3
D2V5, multiclass
                                                                                   clus
vv                                                                                  FRG1 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)            7
  PRIMARY DLBCL OF THE CNS                                                                     0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                           1
                                                                                   clus
vv                                                                                  FRG1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             26
  PRIMARY DLBCL OF THE CNS                                                                       3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FRG1 MUTATED       4                         0     4
  FRG1 WILD-TYPE    14                         1    17
D2V6, multiclass
                           clus
vv                          FRG1 MUTATED FRG1 WILD-TYPE
  ASIAN                                4             14
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                4             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                cls
clus              0  1
  FRG1 MUTATED    0  8
  FRG1 WILD-TYPE 12 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRG1 MUTATED      0    8
  FRG1 WILD-TYPE   12   20
                        clus
vv                       FRG1 MUTATED FRG1 WILD-TYPE
  HISPANIC OR LATINO                0             12
  NOT HISPANIC OR LATINO            8             20
[1] 2 2
[1] FALSE

Clustering(3) Variable = MLL2 MUTATION ANALYSIS
D3V1, survival
                sevent
clus2             0  1
  MLL2 MUTATED   12  2
  MLL2 WILD-TYPE 22  4
  MLL2 MUTATED MLL2 WILD-TYPE 
            14             26 
  MLL2 MUTATED MLL2 WILD-TYPE 
             2              4 
$`MLL2 MUTATED`
TCGA-FA-A4BB TCGA-FA-A7DS TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 
        4.34        23.64        14.04        18.18        31.10        31.73 
TCGA-FF-8047 TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-7353 
        4.14        10.29        26.01        31.96        41.16        98.07 
TCGA-GS-A9TQ TCGA-GS-A9TY 
       32.28       109.58 

$`MLL2 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FF-8041 
        4.34        23.28         1.91        24.62         8.15        35.54 
TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CX TCGA-GR-A4D4 
       24.69        27.35        22.32         9.80        12.66        51.98 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV 
       42.71        43.86        57.17        38.24       128.12        24.00 
TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N 
       53.16        45.14        25.15       111.58        12.85        25.91 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  MLL2 MUTATED MLL2 WILD-TYPE 
          4.14           0.03 
  MLL2 MUTATED MLL2 WILD-TYPE 
        109.58         128.12 
  MLL2 MUTATED MLL2 WILD-TYPE 
        28.555         24.920 
[1] "4.1 - 109.6 (28.6)" "0.0 - 128.1 (24.9)"
[1] "hr=" "1.1"
D3V2, continuous
D3V3, binary
                cls
clus              0  1
  MLL2 MUTATED   10  4
  MLL2 WILD-TYPE 14 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     10    4
  MLL2 WILD-TYPE   14   12
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  FEMALE           10             14
  MALE              4             12
[1] 2 2
[1] FALSE
D3V4, binary
                cls
clus              0  1
  MLL2 MUTATED   14  0
  MLL2 WILD-TYPE 19  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     14    0
  MLL2 WILD-TYPE   19    6
     clus
vv    MLL2 MUTATED MLL2 WILD-TYPE
  NO            14             19
  YES            0              6
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  MLL2 MUTATED                                                                                  14
  MLL2 WILD-TYPE                                                                                19
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  MLL2 MUTATED                          0                                  0
  MLL2 WILD-TYPE                        3                                  4
D3V5, multiclass
                                                                                   clus
vv                                                                                  MLL2 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)           14
  PRIMARY DLBCL OF THE CNS                                                                     0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                           0
                                                                                   clus
vv                                                                                  MLL2 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             19
  PRIMARY DLBCL OF THE CNS                                                                       3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL2 MUTATED       7                         1     6
  MLL2 WILD-TYPE    11                         0    15
D3V6, multiclass
                           clus
vv                          MLL2 MUTATED MLL2 WILD-TYPE
  ASIAN                                7             11
  BLACK OR AFRICAN AMERICAN            1              0
  WHITE                                6             15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                cls
clus              0  1
  MLL2 MUTATED    2 12
  MLL2 WILD-TYPE 10 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      2   12
  MLL2 WILD-TYPE   10   16
                        clus
vv                       MLL2 MUTATED MLL2 WILD-TYPE
  HISPANIC OR LATINO                2             10
  NOT HISPANIC OR LATINO           12             16
[1] 2 2
[1] FALSE

Clustering(4) Variable = TPPP MUTATION ANALYSIS
D4V1, survival
                sevent
clus2             0  1
  TPPP MUTATED    5  0
  TPPP WILD-TYPE 29  6
  TPPP MUTATED TPPP WILD-TYPE 
             5             35 
  TPPP MUTATED TPPP WILD-TYPE 
             0              6 
$`TPPP MUTATED`
TCGA-FA-A6HO TCGA-FA-A86F TCGA-FF-8046 TCGA-GR-7353 TCGA-GR-A4D9 
       24.62        18.18        24.69        98.07        57.17 

$`TPPP WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        23.28         1.91        23.64         8.15 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 
       14.04        35.54        31.10        31.73         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-G8-6324 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GS-A9TQ TCGA-GS-A9TT 
       41.16        51.98        42.71        43.86        32.28        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
      128.12        24.00        53.16        45.14       109.58        25.15 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
      111.58        12.85        25.91         0.03         0.56 

  TPPP MUTATED TPPP WILD-TYPE 
         18.18           0.03 
  TPPP MUTATED TPPP WILD-TYPE 
         98.07         128.12 
  TPPP MUTATED TPPP WILD-TYPE 
         24.69          25.91 
[1] "18.2 - 98.1 (24.7)" "0.0 - 128.1 (25.9)"
[1] "hr="     "2.4e+08"
D4V2, continuous
D4V3, binary
                cls
clus              0  1
  TPPP MUTATED    3  2
  TPPP WILD-TYPE 21 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPPP MUTATED      3    2
  TPPP WILD-TYPE   21   14
        clus
vv       TPPP MUTATED TPPP WILD-TYPE
  FEMALE            3             21
  MALE              2             14
[1] 2 2
[1] FALSE
D4V4, binary
                cls
clus              0  1
  TPPP MUTATED    5  0
  TPPP WILD-TYPE 28  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPPP MUTATED      5    0
  TPPP WILD-TYPE   28    6
     clus
vv    TPPP MUTATED TPPP WILD-TYPE
  NO             5             28
  YES            0              6
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  TPPP MUTATED                                                                                   5
  TPPP WILD-TYPE                                                                                28
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  TPPP MUTATED                          0                                  0
  TPPP WILD-TYPE                        3                                  4
D4V5, multiclass
                                                                                   clus
vv                                                                                  TPPP MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)            5
  PRIMARY DLBCL OF THE CNS                                                                     0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                           0
                                                                                   clus
vv                                                                                  TPPP WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             28
  PRIMARY DLBCL OF THE CNS                                                                       3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TPPP MUTATED       2                         0     3
  TPPP WILD-TYPE    16                         1    18
D4V6, multiclass
                           clus
vv                          TPPP MUTATED TPPP WILD-TYPE
  ASIAN                                2             16
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                3             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                cls
clus              0  1
  TPPP MUTATED    0  5
  TPPP WILD-TYPE 12 23
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPPP MUTATED      0    5
  TPPP WILD-TYPE   12   23
                        clus
vv                       TPPP MUTATED TPPP WILD-TYPE
  HISPANIC OR LATINO                0             12
  NOT HISPANIC OR LATINO            5             23
[1] 2 2
[1] FALSE

Clustering(5) Variable = CHIT1 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2              0  1
  CHIT1 MUTATED    4  2
  CHIT1 WILD-TYPE 30  4
  CHIT1 MUTATED CHIT1 WILD-TYPE 
              6              34 
  CHIT1 MUTATED CHIT1 WILD-TYPE 
              2               4 
$`CHIT1 MUTATED`
TCGA-FA-A6HN TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8046 TCGA-FF-A7CQ TCGA-FF-A7CW 
        1.91         8.15        14.04        24.69         9.80        26.01 

$`CHIT1 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A86F 
        4.34         4.34        23.28        24.62        23.64        18.18 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.10        31.73         4.14        27.35        22.32 
TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D4 
       10.29        12.66        31.96        41.16        98.07        51.98 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU 
       42.71        43.86        57.17        32.28        38.24       128.12 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 
       24.00        53.16        45.14       109.58        25.15       111.58 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85        25.91         0.03         0.56 

  CHIT1 MUTATED CHIT1 WILD-TYPE 
           1.91            0.03 
  CHIT1 MUTATED CHIT1 WILD-TYPE 
          26.01          128.12 
  CHIT1 MUTATED CHIT1 WILD-TYPE 
         11.920          29.225 
[1] "1.9 - 26.0 (11.9)"  "0.0 - 128.1 (29.2)"
[1] "hr=" "5.3"
D5V2, continuous
D5V3, binary
                 cls
clus               0  1
  CHIT1 MUTATED    2  4
  CHIT1 WILD-TYPE 22 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHIT1 MUTATED      2    4
  CHIT1 WILD-TYPE   22   12
        clus
vv       CHIT1 MUTATED CHIT1 WILD-TYPE
  FEMALE             2              22
  MALE               4              12
[1] 2 2
[1] FALSE
D5V4, binary
                 cls
clus               0  1
  CHIT1 MUTATED    6  0
  CHIT1 WILD-TYPE 27  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHIT1 MUTATED      6    0
  CHIT1 WILD-TYPE   27    6
     clus
vv    CHIT1 MUTATED CHIT1 WILD-TYPE
  NO              6              27
  YES             0               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  CHIT1 MUTATED                                                                                   6
  CHIT1 WILD-TYPE                                                                                27
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  CHIT1 MUTATED                          0                                  0
  CHIT1 WILD-TYPE                        3                                  4
D5V5, multiclass
                                                                                   clus
vv                                                                                  CHIT1 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             6
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  CHIT1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              27
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CHIT1 MUTATED       6                         0     0
  CHIT1 WILD-TYPE    12                         1    21
D5V6, multiclass
                           clus
vv                          CHIT1 MUTATED CHIT1 WILD-TYPE
  ASIAN                                 6              12
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 0              21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                 cls
clus               0  1
  CHIT1 MUTATED    0  6
  CHIT1 WILD-TYPE 12 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHIT1 MUTATED      0    6
  CHIT1 WILD-TYPE   12   22
                        clus
vv                       CHIT1 MUTATED CHIT1 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             6              22
[1] 2 2
[1] FALSE

Clustering(6) Variable = B2M MUTATION ANALYSIS
D6V1, survival
               sevent
clus2            0  1
  B2M MUTATED    8  0
  B2M WILD-TYPE 26  6
  B2M MUTATED B2M WILD-TYPE 
            8            32 
  B2M MUTATED B2M WILD-TYPE 
            0             6 
$`B2M MUTATED`
TCGA-FF-8041 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-GR-A4D9 TCGA-GS-A9TV 
       35.54        27.35        22.32        31.96        57.17        24.00 
TCGA-GS-A9TW TCGA-RQ-A6JB 
       53.16         0.03 

$`B2M WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
        8.15        14.04        18.18        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-G8-6324 
        4.14         9.80        10.29        26.01        12.66        41.16 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GS-A9TQ TCGA-GS-A9TT 
       98.07        51.98        42.71        43.86        32.28        38.24 
TCGA-GS-A9TU TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 
      128.12        45.14       109.58        25.15       111.58        12.85 
TCGA-RQ-A68N TCGA-RQ-AAAT 
       25.91         0.56 

  B2M MUTATED B2M WILD-TYPE 
         0.03          0.56 
  B2M MUTATED B2M WILD-TYPE 
        57.17        128.12 
  B2M MUTATED B2M WILD-TYPE 
       29.655        24.920 
[1] "0.0 - 57.2 (29.7)"  "0.6 - 128.1 (24.9)"
[1] "hr="     "2.6e+08"
D6V2, continuous
D6V3, binary
               cls
clus             0  1
  B2M MUTATED    7  1
  B2M WILD-TYPE 17 15
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      7    1
  B2M WILD-TYPE   17   15
        clus
vv       B2M MUTATED B2M WILD-TYPE
  FEMALE           7            17
  MALE             1            15
[1] 2 2
[1] FALSE
D6V4, binary
               cls
clus             0  1
  B2M MUTATED    5  2
  B2M WILD-TYPE 28  4
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      5    2
  B2M WILD-TYPE   28    4
     clus
vv    B2M MUTATED B2M WILD-TYPE
  NO            5            28
  YES           2             4
[1] 2 2
[1] FALSE
               vv
clus            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  B2M MUTATED                                                                                   4
  B2M WILD-TYPE                                                                                29
               vv
clus            PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  B2M MUTATED                          1                                  3
  B2M WILD-TYPE                        2                                  1
D6V5, multiclass
                                                                                   clus
vv                                                                                  B2M MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)           4
  PRIMARY DLBCL OF THE CNS                                                                    1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                          3
                                                                                   clus
vv                                                                                  B2M WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)            29
  PRIMARY DLBCL OF THE CNS                                                                      2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  B2M MUTATED       3                         0     5
  B2M WILD-TYPE    15                         1    16
D6V6, multiclass
                           clus
vv                          B2M MUTATED B2M WILD-TYPE
  ASIAN                               3            15
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                               5            16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
               cls
clus             0  1
  B2M MUTATED    2  6
  B2M WILD-TYPE 10 22
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      2    6
  B2M WILD-TYPE   10   22
                        clus
vv                       B2M MUTATED B2M WILD-TYPE
  HISPANIC OR LATINO               2            10
  NOT HISPANIC OR LATINO           6            22
[1] 2 2
[1] FALSE

Clustering(7) Variable = TPTE2 MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2              0  1
  TPTE2 MUTATED    9  2
  TPTE2 WILD-TYPE 25  4
  TPTE2 MUTATED TPTE2 WILD-TYPE 
             11              29 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
              2               4 
$`TPTE2 MUTATED`
TCGA-FA-A4BB TCGA-FA-A6HO TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CX TCGA-G8-6324 
        4.34        24.62         9.80        10.29        12.66        41.16 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TU TCGA-RQ-A68N TCGA-RQ-AAAT 
       43.86        57.17       128.12        25.91         0.56 

$`TPTE2 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34        23.28         1.91        23.64         8.15        14.04 
TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       18.18        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CW TCGA-FM-8000 TCGA-GR-7353 TCGA-GR-A4D4 
       27.35        22.32        26.01        31.96        98.07        51.98 
TCGA-GR-A4D5 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       42.71        32.28        38.24        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85         0.03 

  TPTE2 MUTATED TPTE2 WILD-TYPE 
           0.56            0.03 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
         128.12          111.58 
  TPTE2 MUTATED TPTE2 WILD-TYPE 
          24.62           26.01 
[1] "0.6 - 128.1 (24.6)" "0.0 - 111.6 (26.0)"
[1] "hr=" "1.4"
D7V2, continuous
D7V3, binary
                 cls
clus               0  1
  TPTE2 MUTATED    5  6
  TPTE2 WILD-TYPE 19 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      5    6
  TPTE2 WILD-TYPE   19   10
        clus
vv       TPTE2 MUTATED TPTE2 WILD-TYPE
  FEMALE             5              19
  MALE               6              10
[1] 2 2
[1] FALSE
D7V4, binary
                 cls
clus               0  1
  TPTE2 MUTATED   10  1
  TPTE2 WILD-TYPE 23  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED     10    1
  TPTE2 WILD-TYPE   23    5
     clus
vv    TPTE2 MUTATED TPTE2 WILD-TYPE
  NO             10              23
  YES             1               5
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  TPTE2 MUTATED                                                                                   9
  TPTE2 WILD-TYPE                                                                                24
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  TPTE2 MUTATED                          2                                  0
  TPTE2 WILD-TYPE                        1                                  4
D7V5, multiclass
                                                                                   clus
vv                                                                                  TPTE2 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             9
  PRIMARY DLBCL OF THE CNS                                                                      2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  TPTE2 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              24
  PRIMARY DLBCL OF THE CNS                                                                        1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TPTE2 MUTATED       5                         1     5
  TPTE2 WILD-TYPE    13                         0    16
D7V6, multiclass
                           clus
vv                          TPTE2 MUTATED TPTE2 WILD-TYPE
  ASIAN                                 5              13
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 5              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                 cls
clus               0  1
  TPTE2 MUTATED    3  8
  TPTE2 WILD-TYPE  9 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPTE2 MUTATED      3    8
  TPTE2 WILD-TYPE    9   20
                        clus
vv                       TPTE2 MUTATED TPTE2 WILD-TYPE
  HISPANIC OR LATINO                 3               9
  NOT HISPANIC OR LATINO             8              20
[1] 2 2
[1] FALSE

Clustering(8) Variable = RHPN2 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2              0  1
  RHPN2 MUTATED    5  1
  RHPN2 WILD-TYPE 29  5
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              6              34 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              1               5 
$`RHPN2 MUTATED`
TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8061 TCGA-G8-6324 TCGA-GS-A9TU 
       35.54        31.73        24.69        27.35        41.16       128.12 

$`RHPN2 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8047 TCGA-FF-8062 
        8.15        14.04        18.18        31.10         4.14        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-7353 
        9.80        10.29        26.01        12.66        31.96        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT 
       51.98        42.71        43.86        57.17        32.28        38.24 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 
       24.00        53.16        45.14       109.58        25.15       111.58 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85        25.91         0.03         0.56 

  RHPN2 MUTATED RHPN2 WILD-TYPE 
          24.69            0.03 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
         128.12          111.58 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
         33.635          24.310 
[1] "24.7 - 128.1 (33.6)" "0.0 - 111.6 (24.3)" 
[1] "hr=" "1.2"
D8V2, continuous
D8V3, binary
                 cls
clus               0  1
  RHPN2 MUTATED    3  3
  RHPN2 WILD-TYPE 21 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED      3    3
  RHPN2 WILD-TYPE   21   13
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  FEMALE             3              21
  MALE               3              13
[1] 2 2
[1] FALSE
D8V4, binary
                 cls
clus               0  1
  RHPN2 MUTATED    5  1
  RHPN2 WILD-TYPE 28  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED      5    1
  RHPN2 WILD-TYPE   28    5
     clus
vv    RHPN2 MUTATED RHPN2 WILD-TYPE
  NO              5              28
  YES             1               5
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  RHPN2 MUTATED                                                                                   5
  RHPN2 WILD-TYPE                                                                                28
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  RHPN2 MUTATED                          0                                  1
  RHPN2 WILD-TYPE                        3                                  3
D8V5, multiclass
                                                                                   clus
vv                                                                                  RHPN2 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             5
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            1
                                                                                   clus
vv                                                                                  RHPN2 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              28
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RHPN2 MUTATED       4                         1     1
  RHPN2 WILD-TYPE    14                         0    20
D8V6, multiclass
                           clus
vv                          RHPN2 MUTATED RHPN2 WILD-TYPE
  ASIAN                                 4              14
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 1              20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                 cls
clus               0  1
  RHPN2 MUTATED    1  5
  RHPN2 WILD-TYPE 11 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED      1    5
  RHPN2 WILD-TYPE   11   23
                        clus
vv                       RHPN2 MUTATED RHPN2 WILD-TYPE
  HISPANIC OR LATINO                 1              11
  NOT HISPANIC OR LATINO             5              23
[1] 2 2
[1] FALSE

Clustering(9) Variable = FOXD4L1 MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  FOXD4L1 MUTATED    5  2
  FOXD4L1 WILD-TYPE 29  4
  FOXD4L1 MUTATED FOXD4L1 WILD-TYPE 
                7                33 
  FOXD4L1 MUTATED FOXD4L1 WILD-TYPE 
                2                 4 
$`FOXD4L1 MUTATED`
TCGA-FA-A4BB TCGA-FA-A82F TCGA-FF-A7CR TCGA-G8-6324 TCGA-GR-A4D4 TCGA-GR-A4D9 
        4.34        14.04        10.29        41.16        51.98        57.17 
TCGA-GS-A9TW 
       53.16 

$`FOXD4L1 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34        23.28         1.91        24.62        23.64         8.15 
TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       18.18        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       27.35        22.32         9.80        26.01        12.66        31.96 
TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU 
       98.07        42.71        43.86        32.28        38.24       128.12 
TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 
       24.00        45.14       109.58        25.15       111.58        12.85 
TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.91         0.03         0.56 

  FOXD4L1 MUTATED FOXD4L1 WILD-TYPE 
             4.34              0.03 
  FOXD4L1 MUTATED FOXD4L1 WILD-TYPE 
            57.17            128.12 
  FOXD4L1 MUTATED FOXD4L1 WILD-TYPE 
            41.16             25.15 
[1] "4.3 - 57.2 (41.2)"  "0.0 - 128.1 (25.1)"
[1] "hr=" "2"  
D9V2, continuous
D9V3, binary
                   cls
clus                 0  1
  FOXD4L1 MUTATED    5  2
  FOXD4L1 WILD-TYPE 19 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FOXD4L1 MUTATED      5    2
  FOXD4L1 WILD-TYPE   19   14
        clus
vv       FOXD4L1 MUTATED FOXD4L1 WILD-TYPE
  FEMALE               5                19
  MALE                 2                14
[1] 2 2
[1] FALSE
D9V4, binary
                   cls
clus                 0  1
  FOXD4L1 MUTATED    6  1
  FOXD4L1 WILD-TYPE 27  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FOXD4L1 MUTATED      6    1
  FOXD4L1 WILD-TYPE   27    5
     clus
vv    FOXD4L1 MUTATED FOXD4L1 WILD-TYPE
  NO                6                27
  YES               1                 5
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  FOXD4L1 MUTATED                                                                                   6
  FOXD4L1 WILD-TYPE                                                                                27
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  FOXD4L1 MUTATED                          0                                  1
  FOXD4L1 WILD-TYPE                        3                                  3
D9V5, multiclass
                                                                                   clus
vv                                                                                  FOXD4L1 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               6
  PRIMARY DLBCL OF THE CNS                                                                        0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              1
                                                                                   clus
vv                                                                                  FOXD4L1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                27
  PRIMARY DLBCL OF THE CNS                                                                          3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FOXD4L1 MUTATED       2                         1     4
  FOXD4L1 WILD-TYPE    16                         0    17
D9V6, multiclass
                           clus
vv                          FOXD4L1 MUTATED FOXD4L1 WILD-TYPE
  ASIAN                                   2                16
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                   4                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                   cls
clus                 0  1
  FOXD4L1 MUTATED    1  6
  FOXD4L1 WILD-TYPE 11 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FOXD4L1 MUTATED      1    6
  FOXD4L1 WILD-TYPE   11   22
                        clus
vv                       FOXD4L1 MUTATED FOXD4L1 WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               6                22
[1] 2 2
[1] FALSE

Clustering(10) Variable = DND1 MUTATION ANALYSIS
D10V1, survival
                sevent
clus2             0  1
  DND1 MUTATED    4  0
  DND1 WILD-TYPE 30  6
  DND1 MUTATED DND1 WILD-TYPE 
             4             36 
  DND1 MUTATED DND1 WILD-TYPE 
             0              6 
$`DND1 MUTATED`
TCGA-FA-A4BB TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D9 
        4.34        31.96        51.98        57.17 

$`DND1 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34        23.28         1.91        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GS-A9TQ 
       12.66        41.16        98.07        42.71        43.86        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  DND1 MUTATED DND1 WILD-TYPE 
          4.34           0.03 
  DND1 MUTATED DND1 WILD-TYPE 
         57.17         128.12 
  DND1 MUTATED DND1 WILD-TYPE 
         41.97          24.92 
[1] "4.3 - 57.2 (42.0)"  "0.0 - 128.1 (24.9)"
[1] "hr="     "8.1e+07"
D10V2, continuous
D10V3, binary
                cls
clus              0  1
  DND1 MUTATED    3  1
  DND1 WILD-TYPE 21 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  DND1 MUTATED      3    1
  DND1 WILD-TYPE   21   15
        clus
vv       DND1 MUTATED DND1 WILD-TYPE
  FEMALE            3             21
  MALE              1             15
[1] 2 2
[1] FALSE
D10V4, binary
                cls
clus              0  1
  DND1 MUTATED    4  0
  DND1 WILD-TYPE 29  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  DND1 MUTATED      4    0
  DND1 WILD-TYPE   29    6
     clus
vv    DND1 MUTATED DND1 WILD-TYPE
  NO             4             29
  YES            0              6
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DND1 MUTATED                                                                                   4
  DND1 WILD-TYPE                                                                                29
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DND1 MUTATED                          0                                  0
  DND1 WILD-TYPE                        3                                  4
D10V5, multiclass
                                                                                   clus
vv                                                                                  DND1 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)            4
  PRIMARY DLBCL OF THE CNS                                                                     0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                           0
                                                                                   clus
vv                                                                                  DND1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             29
  PRIMARY DLBCL OF THE CNS                                                                       3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DND1 MUTATED       0                         0     4
  DND1 WILD-TYPE    18                         1    17
D10V6, multiclass
                           clus
vv                          DND1 MUTATED DND1 WILD-TYPE
  ASIAN                                0             18
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                4             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                cls
clus              0  1
  DND1 MUTATED    0  4
  DND1 WILD-TYPE 12 24
[1] "tbl2"
                cls
clus             [,1] [,2]
  DND1 MUTATED      0    4
  DND1 WILD-TYPE   12   24
                        clus
vv                       DND1 MUTATED DND1 WILD-TYPE
  HISPANIC OR LATINO                0             12
  NOT HISPANIC OR LATINO            4             24
[1] 2 2
[1] FALSE

Clustering(11) Variable = ATXN1 MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2              0  1
  ATXN1 MUTATED    6  1
  ATXN1 WILD-TYPE 28  5
  ATXN1 MUTATED ATXN1 WILD-TYPE 
              7              33 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
              1               5 
$`ATXN1 MUTATED`
TCGA-FA-A7DS TCGA-FF-8043 TCGA-FF-A7CX TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D4 
       23.64        31.73        12.66        41.16        98.07        51.98 
TCGA-GS-A9TV 
       24.00 

$`ATXN1 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7Q1 
        4.34         4.34        23.28         1.91        24.62         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 
       14.04        18.18        35.54        31.10        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FM-8000 
       27.35        22.32         9.80        10.29        26.01        31.96 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU 
       42.71        43.86        57.17        32.28        38.24       128.12 
TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 
       53.16        45.14       109.58        25.15       111.58        12.85 
TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.91         0.03         0.56 

  ATXN1 MUTATED ATXN1 WILD-TYPE 
          12.66            0.03 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
          98.07          128.12 
  ATXN1 MUTATED ATXN1 WILD-TYPE 
          31.73           25.15 
[1] "12.7 - 98.1 (31.7)" "0.0 - 128.1 (25.1)"
[1] "hr=" "1.4"
D11V2, continuous
D11V3, binary
                 cls
clus               0  1
  ATXN1 MUTATED    5  2
  ATXN1 WILD-TYPE 19 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      5    2
  ATXN1 WILD-TYPE   19   14
        clus
vv       ATXN1 MUTATED ATXN1 WILD-TYPE
  FEMALE             5              19
  MALE               2              14
[1] 2 2
[1] FALSE
D11V4, binary
                 cls
clus               0  1
  ATXN1 MUTATED    6  1
  ATXN1 WILD-TYPE 27  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      6    1
  ATXN1 WILD-TYPE   27    5
     clus
vv    ATXN1 MUTATED ATXN1 WILD-TYPE
  NO              6              27
  YES             1               5
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  ATXN1 MUTATED                                                                                   6
  ATXN1 WILD-TYPE                                                                                27
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  ATXN1 MUTATED                          0                                  1
  ATXN1 WILD-TYPE                        3                                  3
D11V5, multiclass
                                                                                   clus
vv                                                                                  ATXN1 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             6
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            1
                                                                                   clus
vv                                                                                  ATXN1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              27
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATXN1 MUTATED       3                         1     3
  ATXN1 WILD-TYPE    15                         0    18
D11V6, multiclass
                           clus
vv                          ATXN1 MUTATED ATXN1 WILD-TYPE
  ASIAN                                 3              15
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 3              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                 cls
clus               0  1
  ATXN1 MUTATED    1  6
  ATXN1 WILD-TYPE 11 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATXN1 MUTATED      1    6
  ATXN1 WILD-TYPE   11   22
                        clus
vv                       ATXN1 MUTATED ATXN1 WILD-TYPE
  HISPANIC OR LATINO                 1              11
  NOT HISPANIC OR LATINO             6              22
[1] 2 2
[1] FALSE

Clustering(12) Variable = TP53 MUTATION ANALYSIS
D12V1, survival
                sevent
clus2             0  1
  TP53 MUTATED    6  0
  TP53 WILD-TYPE 28  6
  TP53 MUTATED TP53 WILD-TYPE 
             6             34 
  TP53 MUTATED TP53 WILD-TYPE 
             0              6 
$`TP53 MUTATED`
TCGA-FA-A82F TCGA-FF-8043 TCGA-GR-A4D4 TCGA-GS-A9TV TCGA-GS-A9TY TCGA-RQ-AAAT 
       14.04        31.73        51.98        24.00       109.58         0.56 

$`TP53 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 
        8.15        18.18        35.54        31.10        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       31.96        41.16        98.07        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TZ 
       32.28        38.24       128.12        53.16        45.14        25.15 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      111.58        12.85        25.91         0.03 

  TP53 MUTATED TP53 WILD-TYPE 
          0.56           0.03 
  TP53 MUTATED TP53 WILD-TYPE 
        109.58         128.12 
  TP53 MUTATED TP53 WILD-TYPE 
        27.865         25.530 
[1] "0.6 - 109.6 (27.9)" "0.0 - 128.1 (25.5)"
[1] "hr="     "2.4e+08"
D12V2, continuous
D12V3, binary
                cls
clus              0  1
  TP53 MUTATED    6  0
  TP53 WILD-TYPE 18 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      6    0
  TP53 WILD-TYPE   18   16
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            6             18
  MALE              0             16
[1] 2 2
[1] FALSE
D12V4, binary
                cls
clus              0  1
  TP53 MUTATED    5  1
  TP53 WILD-TYPE 28  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      5    1
  TP53 WILD-TYPE   28    5
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO             5             28
  YES            1              5
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  TP53 MUTATED                                                                                   4
  TP53 WILD-TYPE                                                                                29
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  TP53 MUTATED                          1                                  1
  TP53 WILD-TYPE                        2                                  3
D12V5, multiclass
                                                                                   clus
vv                                                                                  TP53 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)            4
  PRIMARY DLBCL OF THE CNS                                                                     1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                           1
                                                                                   clus
vv                                                                                  TP53 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             29
  PRIMARY DLBCL OF THE CNS                                                                       2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       2                         0     4
  TP53 WILD-TYPE    16                         1    17
D12V6, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                2             16
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                4             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                cls
clus              0  1
  TP53 MUTATED    3  3
  TP53 WILD-TYPE  9 25
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      3    3
  TP53 WILD-TYPE    9   25
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                3              9
  NOT HISPANIC OR LATINO            3             25
[1] 2 2
[1] FALSE

Clustering(13) Variable = CDC27 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2              0  1
  CDC27 MUTATED    9  1
  CDC27 WILD-TYPE 25  5
  CDC27 MUTATED CDC27 WILD-TYPE 
             10              30 
  CDC27 MUTATED CDC27 WILD-TYPE 
              1               5 
$`CDC27 MUTATED`
TCGA-FA-8693 TCGA-FF-8043 TCGA-FF-8047 TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-7353 
        4.34        31.73         4.14        31.96        41.16        98.07 
TCGA-GR-A4D5 TCGA-GS-A9TV TCGA-GS-A9TX TCGA-RQ-A6JB 
       42.71        24.00        45.14         0.03 

$`CDC27 WILD-TYPE`
TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34        23.28         1.91        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8061 
       14.04        18.18        35.54        31.10        24.69        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-GR-A4D4 
       22.32         9.80        10.29        26.01        12.66        51.98 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TW 
       43.86        57.17        32.28        38.24       128.12        53.16 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-AAAT 
      109.58        25.15       111.58        12.85        25.91         0.56 

  CDC27 MUTATED CDC27 WILD-TYPE 
           0.03            0.56 
  CDC27 MUTATED CDC27 WILD-TYPE 
          98.07          128.12 
  CDC27 MUTATED CDC27 WILD-TYPE 
         31.845          24.920 
[1] "0.0 - 98.1 (31.8)"  "0.6 - 128.1 (24.9)"
[1] "hr=" "1.7"
D13V2, continuous
D13V3, binary
                 cls
clus               0  1
  CDC27 MUTATED    7  3
  CDC27 WILD-TYPE 17 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      7    3
  CDC27 WILD-TYPE   17   13
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  FEMALE             7              17
  MALE               3              13
[1] 2 2
[1] FALSE
D13V4, binary
                 cls
clus               0  1
  CDC27 MUTATED    7  2
  CDC27 WILD-TYPE 26  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      7    2
  CDC27 WILD-TYPE   26    4
     clus
vv    CDC27 MUTATED CDC27 WILD-TYPE
  NO              7              26
  YES             2               4
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  CDC27 MUTATED                                                                                   8
  CDC27 WILD-TYPE                                                                                25
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  CDC27 MUTATED                          1                                  1
  CDC27 WILD-TYPE                        2                                  3
D13V5, multiclass
                                                                                   clus
vv                                                                                  CDC27 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             8
  PRIMARY DLBCL OF THE CNS                                                                      1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            1
                                                                                   clus
vv                                                                                  CDC27 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              25
  PRIMARY DLBCL OF THE CNS                                                                        2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDC27 MUTATED       2                         1     7
  CDC27 WILD-TYPE    16                         0    14
D13V6, multiclass
                           clus
vv                          CDC27 MUTATED CDC27 WILD-TYPE
  ASIAN                                 2              16
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 7              14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                 cls
clus               0  1
  CDC27 MUTATED    2  8
  CDC27 WILD-TYPE 10 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      2    8
  CDC27 WILD-TYPE   10   20
                        clus
vv                       CDC27 MUTATED CDC27 WILD-TYPE
  HISPANIC OR LATINO                 2              10
  NOT HISPANIC OR LATINO             8              20
[1] 2 2
[1] FALSE

Clustering(14) Variable = EPB41L4A MUTATION ANALYSIS
D14V1, survival
                    sevent
clus2                 0  1
  EPB41L4A MUTATED    4  0
  EPB41L4A WILD-TYPE 30  6
  EPB41L4A MUTATED EPB41L4A WILD-TYPE 
                 4                 36 
  EPB41L4A MUTATED EPB41L4A WILD-TYPE 
                 0                  6 
$`EPB41L4A MUTATED`
TCGA-FA-A7DS TCGA-FF-8062 TCGA-GR-7353 TCGA-GS-A9TV 
       23.64        22.32        98.07        24.00 

$`EPB41L4A WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7Q1 
        4.34         4.34        23.28         1.91        24.62         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
        4.14        27.35         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       31.96        41.16        51.98        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       32.28        38.24       128.12        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  EPB41L4A MUTATED EPB41L4A WILD-TYPE 
             22.32               0.03 
  EPB41L4A MUTATED EPB41L4A WILD-TYPE 
             98.07             128.12 
  EPB41L4A MUTATED EPB41L4A WILD-TYPE 
             23.82              25.96 
[1] "22.3 - 98.1 (23.8)" "0.0 - 128.1 (26.0)"
[1] "hr="   "8e+07"
D14V2, continuous
D14V3, binary
                    cls
clus                  0  1
  EPB41L4A MUTATED    3  1
  EPB41L4A WILD-TYPE 21 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4A MUTATED      3    1
  EPB41L4A WILD-TYPE   21   15
        clus
vv       EPB41L4A MUTATED EPB41L4A WILD-TYPE
  FEMALE                3                 21
  MALE                  1                 15
[1] 2 2
[1] FALSE
D14V4, binary
                    cls
clus                  0  1
  EPB41L4A MUTATED    3  1
  EPB41L4A WILD-TYPE 30  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4A MUTATED      3    1
  EPB41L4A WILD-TYPE   30    5
     clus
vv    EPB41L4A MUTATED EPB41L4A WILD-TYPE
  NO                 3                 30
  YES                1                  5
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  EPB41L4A MUTATED                                                                                   3
  EPB41L4A WILD-TYPE                                                                                30
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  EPB41L4A MUTATED                          0
  EPB41L4A WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  EPB41L4A MUTATED                                    1
  EPB41L4A WILD-TYPE                                  3
D14V5, multiclass
                                                                                   clus
vv                                                                                  EPB41L4A MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                3
  PRIMARY DLBCL OF THE CNS                                                                         0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               1
                                                                                   clus
vv                                                                                  EPB41L4A WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 30
  PRIMARY DLBCL OF THE CNS                                                                           3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EPB41L4A MUTATED       2                         0     2
  EPB41L4A WILD-TYPE    16                         1    19
D14V6, multiclass
                           clus
vv                          EPB41L4A MUTATED EPB41L4A WILD-TYPE
  ASIAN                                    2                 16
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                    cls
clus                  0  1
  EPB41L4A MUTATED    1  3
  EPB41L4A WILD-TYPE 11 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  EPB41L4A MUTATED      1    3
  EPB41L4A WILD-TYPE   11   25
                        clus
vv                       EPB41L4A MUTATED EPB41L4A WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO                3                 25
[1] 2 2
[1] FALSE

Clustering(15) Variable = NOTCH2NL MUTATION ANALYSIS
D15V1, survival
                    sevent
clus2                 0  1
  NOTCH2NL MUTATED    3  1
  NOTCH2NL WILD-TYPE 31  5
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 4                 36 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 1                  5 
$`NOTCH2NL MUTATED`
TCGA-FA-A86F TCGA-G8-6324 TCGA-GS-A9TU TCGA-RQ-AAAT 
       18.18        41.16       128.12         0.56 

$`NOTCH2NL WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
        8.15        14.04        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
       12.66        31.96        98.07        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       57.17        32.28        38.24        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 

  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
              0.56               0.03 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
            128.12             111.58 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
             29.67              25.53 
[1] "0.6 - 128.1 (29.7)" "0.0 - 111.6 (25.5)"
[1] "hr=" "1.8"
D15V2, continuous
D15V3, binary
                    cls
clus                  0  1
  NOTCH2NL MUTATED    3  1
  NOTCH2NL WILD-TYPE 21 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      3    1
  NOTCH2NL WILD-TYPE   21   15
        clus
vv       NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  FEMALE                3                 21
  MALE                  1                 15
[1] 2 2
[1] FALSE
D15V4, binary
                    cls
clus                  0  1
  NOTCH2NL MUTATED    3  1
  NOTCH2NL WILD-TYPE 30  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      3    1
  NOTCH2NL WILD-TYPE   30    5
     clus
vv    NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  NO                 3                 30
  YES                1                  5
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  NOTCH2NL MUTATED                                                                                   3
  NOTCH2NL WILD-TYPE                                                                                30
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  NOTCH2NL MUTATED                          1
  NOTCH2NL WILD-TYPE                        2
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  NOTCH2NL MUTATED                                    0
  NOTCH2NL WILD-TYPE                                  4
D15V5, multiclass
                                                                                   clus
vv                                                                                  NOTCH2NL MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                3
  PRIMARY DLBCL OF THE CNS                                                                         1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               0
                                                                                   clus
vv                                                                                  NOTCH2NL WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 30
  PRIMARY DLBCL OF THE CNS                                                                           2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NOTCH2NL MUTATED       0                         1     3
  NOTCH2NL WILD-TYPE    18                         0    18
D15V6, multiclass
                           clus
vv                          NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  ASIAN                                    0                 18
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                    3                 18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                    cls
clus                  0  1
  NOTCH2NL MUTATED    2  2
  NOTCH2NL WILD-TYPE 10 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      2    2
  NOTCH2NL WILD-TYPE   10   26
                        clus
vv                       NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                2                 26
[1] 2 2
[1] FALSE

Clustering(16) Variable = KRT3 MUTATION ANALYSIS
D16V1, survival
                sevent
clus2             0  1
  KRT3 MUTATED    2  2
  KRT3 WILD-TYPE 32  4
  KRT3 MUTATED KRT3 WILD-TYPE 
             4             36 
  KRT3 MUTATED KRT3 WILD-TYPE 
             2              4 
$`KRT3 MUTATED`
TCGA-FA-A7Q1 TCGA-FF-8062 TCGA-G8-6324 TCGA-GS-A9TQ 
        8.15        22.32        41.16        32.28 

$`KRT3 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
        4.14        27.35         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       31.96        98.07        51.98        42.71        43.86        57.17 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  KRT3 MUTATED KRT3 WILD-TYPE 
          8.15           0.03 
  KRT3 MUTATED KRT3 WILD-TYPE 
         41.16         128.12 
  KRT3 MUTATED KRT3 WILD-TYPE 
         27.30          25.53 
[1] "8.2 - 41.2 (27.3)"  "0.0 - 128.1 (25.5)"
[1] "hr=" "4.7"
D16V2, continuous
D16V3, binary
                cls
clus              0  1
  KRT3 MUTATED    4  0
  KRT3 WILD-TYPE 20 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT3 MUTATED      4    0
  KRT3 WILD-TYPE   20   16
        clus
vv       KRT3 MUTATED KRT3 WILD-TYPE
  FEMALE            4             20
  MALE              0             16
[1] 2 2
[1] FALSE
D16V4, binary
                cls
clus              0  1
  KRT3 MUTATED    4  0
  KRT3 WILD-TYPE 29  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT3 MUTATED      4    0
  KRT3 WILD-TYPE   29    6
     clus
vv    KRT3 MUTATED KRT3 WILD-TYPE
  NO             4             29
  YES            0              6
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  KRT3 MUTATED                                                                                   4
  KRT3 WILD-TYPE                                                                                29
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  KRT3 MUTATED                          0                                  0
  KRT3 WILD-TYPE                        3                                  4
D16V5, multiclass
                                                                                   clus
vv                                                                                  KRT3 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)            4
  PRIMARY DLBCL OF THE CNS                                                                     0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                           0
                                                                                   clus
vv                                                                                  KRT3 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             29
  PRIMARY DLBCL OF THE CNS                                                                       3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRT3 MUTATED       2                         1     1
  KRT3 WILD-TYPE    16                         0    20
D16V6, multiclass
                           clus
vv                          KRT3 MUTATED KRT3 WILD-TYPE
  ASIAN                                2             16
  BLACK OR AFRICAN AMERICAN            1              0
  WHITE                                1             20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                cls
clus              0  1
  KRT3 MUTATED    1  3
  KRT3 WILD-TYPE 11 25
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT3 MUTATED      1    3
  KRT3 WILD-TYPE   11   25
                        clus
vv                       KRT3 MUTATED KRT3 WILD-TYPE
  HISPANIC OR LATINO                1             11
  NOT HISPANIC OR LATINO            3             25
[1] 2 2
[1] FALSE

Clustering(17) Variable = OR1S2 MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2              0  1
  OR1S2 MUTATED    9  1
  OR1S2 WILD-TYPE 25  5
  OR1S2 MUTATED OR1S2 WILD-TYPE 
             10              30 
  OR1S2 MUTATED OR1S2 WILD-TYPE 
              1               5 
$`OR1S2 MUTATED`
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-A7CQ TCGA-FF-A7CW 
       14.04        18.18        24.69        27.35         9.80        26.01 
TCGA-G8-6324 TCGA-GR-A4D9 TCGA-GS-A9TU TCGA-RQ-A6JB 
       41.16        57.17       128.12         0.03 

$`OR1S2 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8062 
        8.15        35.54        31.10        31.73         4.14        22.32 
TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
       10.29        12.66        31.96        98.07        51.98        42.71 
TCGA-GR-A4D6 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       43.86        32.28        38.24        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-AAAT 
      109.58        25.15       111.58        12.85        25.91         0.56 

  OR1S2 MUTATED OR1S2 WILD-TYPE 
           0.03            0.56 
  OR1S2 MUTATED OR1S2 WILD-TYPE 
         128.12          111.58 
  OR1S2 MUTATED OR1S2 WILD-TYPE 
          25.35           25.53 
[1] "0.0 - 128.1 (25.4)" "0.6 - 111.6 (25.5)"
[1] "hr=" "1.7"
D17V2, continuous
D17V3, binary
                 cls
clus               0  1
  OR1S2 MUTATED    5  5
  OR1S2 WILD-TYPE 19 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1S2 MUTATED      5    5
  OR1S2 WILD-TYPE   19   11
        clus
vv       OR1S2 MUTATED OR1S2 WILD-TYPE
  FEMALE             5              19
  MALE               5              11
[1] 2 2
[1] FALSE
D17V4, binary
                 cls
clus               0  1
  OR1S2 MUTATED    8  1
  OR1S2 WILD-TYPE 25  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1S2 MUTATED      8    1
  OR1S2 WILD-TYPE   25    5
     clus
vv    OR1S2 MUTATED OR1S2 WILD-TYPE
  NO              8              25
  YES             1               5
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  OR1S2 MUTATED                                                                                   9
  OR1S2 WILD-TYPE                                                                                24
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  OR1S2 MUTATED                          1                                  0
  OR1S2 WILD-TYPE                        2                                  4
D17V5, multiclass
                                                                                   clus
vv                                                                                  OR1S2 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             9
  PRIMARY DLBCL OF THE CNS                                                                      1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  OR1S2 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              24
  PRIMARY DLBCL OF THE CNS                                                                        2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR1S2 MUTATED       5                         1     4
  OR1S2 WILD-TYPE    13                         0    17
D17V6, multiclass
                           clus
vv                          OR1S2 MUTATED OR1S2 WILD-TYPE
  ASIAN                                 5              13
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 4              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                 cls
clus               0  1
  OR1S2 MUTATED    1  9
  OR1S2 WILD-TYPE 11 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1S2 MUTATED      1    9
  OR1S2 WILD-TYPE   11   19
                        clus
vv                       OR1S2 MUTATED OR1S2 WILD-TYPE
  HISPANIC OR LATINO                 1              11
  NOT HISPANIC OR LATINO             9              19
[1] 2 2
[1] FALSE

Clustering(18) Variable = RGPD5 MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2              0  1
  RGPD5 MUTATED    2  3
  RGPD5 WILD-TYPE 32  3
  RGPD5 MUTATED RGPD5 WILD-TYPE 
              5              35 
  RGPD5 MUTATED RGPD5 WILD-TYPE 
              3               3 
$`RGPD5 MUTATED`
TCGA-FA-8693 TCGA-FF-A7CR TCGA-G8-6324 TCGA-GS-A9TW TCGA-GS-A9U4 
        4.34        10.29        41.16        53.16        12.85 

$`RGPD5 WILD-TYPE`
TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34        23.28         1.91        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CW TCGA-FF-A7CX 
        4.14        27.35        22.32         9.80        26.01        12.66 
TCGA-FM-8000 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       31.96        98.07        51.98        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9TY 
       32.28        38.24       128.12        24.00        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        25.91         0.03         0.56 

  RGPD5 MUTATED RGPD5 WILD-TYPE 
           4.34            0.03 
  RGPD5 MUTATED RGPD5 WILD-TYPE 
          53.16          128.12 
  RGPD5 MUTATED RGPD5 WILD-TYPE 
          12.85           25.91 
[1] "4.3 - 53.2 (12.8)"  "0.0 - 128.1 (25.9)"
[1] "hr=" "7.4"
D18V2, continuous
D18V3, binary
                 cls
clus               0  1
  RGPD5 MUTATED    3  2
  RGPD5 WILD-TYPE 21 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGPD5 MUTATED      3    2
  RGPD5 WILD-TYPE   21   14
        clus
vv       RGPD5 MUTATED RGPD5 WILD-TYPE
  FEMALE             3              21
  MALE               2              14
[1] 2 2
[1] FALSE
D18V4, binary
                 cls
clus               0  1
  RGPD5 MUTATED    4  1
  RGPD5 WILD-TYPE 29  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGPD5 MUTATED      4    1
  RGPD5 WILD-TYPE   29    5
     clus
vv    RGPD5 MUTATED RGPD5 WILD-TYPE
  NO              4              29
  YES             1               5
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  RGPD5 MUTATED                                                                                   4
  RGPD5 WILD-TYPE                                                                                29
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  RGPD5 MUTATED                          0                                  1
  RGPD5 WILD-TYPE                        3                                  3
D18V5, multiclass
                                                                                   clus
vv                                                                                  RGPD5 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             4
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            1
                                                                                   clus
vv                                                                                  RGPD5 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              29
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RGPD5 MUTATED       1                         1     3
  RGPD5 WILD-TYPE    17                         0    18
D18V6, multiclass
                           clus
vv                          RGPD5 MUTATED RGPD5 WILD-TYPE
  ASIAN                                 1              17
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 3              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                 cls
clus               0  1
  RGPD5 MUTATED    2  3
  RGPD5 WILD-TYPE 10 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGPD5 MUTATED      2    3
  RGPD5 WILD-TYPE   10   25
                        clus
vv                       RGPD5 MUTATED RGPD5 WILD-TYPE
  HISPANIC OR LATINO                 2              10
  NOT HISPANIC OR LATINO             3              25
[1] 2 2
[1] FALSE

Clustering(19) Variable = TNFAIP3 MUTATION ANALYSIS
D19V1, survival
                   sevent
clus2                0  1
  TNFAIP3 MUTATED    4  2
  TNFAIP3 WILD-TYPE 30  4
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
                6                34 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
                2                 4 
$`TNFAIP3 MUTATED`
TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-A7CR TCGA-FF-A7CX TCGA-G8-6324 TCGA-GS-A9TZ 
       18.18        35.54        10.29        12.66        41.16        25.15 

$`TNFAIP3 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
        8.15        14.04        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CW TCGA-FM-8000 TCGA-GR-7353 
       27.35        22.32         9.80        26.01        31.96        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT 
       51.98        42.71        43.86        57.17        32.28        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9U3 
      128.12        24.00        53.16        45.14       109.58       111.58 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85        25.91         0.03         0.56 

  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
            10.29              0.03 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
            41.16            128.12 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
           21.665            25.960 
[1] "10.3 - 41.2 (21.7)" "0.0 - 128.1 (26.0)"
[1] "hr=" "3"  
D19V2, continuous
D19V3, binary
                   cls
clus                 0  1
  TNFAIP3 MUTATED    3  3
  TNFAIP3 WILD-TYPE 21 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED      3    3
  TNFAIP3 WILD-TYPE   21   13
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  FEMALE               3                21
  MALE                 3                13
[1] 2 2
[1] FALSE
D19V4, binary
                   cls
clus                 0  1
  TNFAIP3 MUTATED    5  1
  TNFAIP3 WILD-TYPE 28  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED      5    1
  TNFAIP3 WILD-TYPE   28    5
     clus
vv    TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  NO                5                28
  YES               1                 5
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  TNFAIP3 MUTATED                                                                                   4
  TNFAIP3 WILD-TYPE                                                                                29
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  TNFAIP3 MUTATED                          0                                  2
  TNFAIP3 WILD-TYPE                        3                                  2
D19V5, multiclass
                                                                                   clus
vv                                                                                  TNFAIP3 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               4
  PRIMARY DLBCL OF THE CNS                                                                        0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              2
                                                                                   clus
vv                                                                                  TNFAIP3 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                29
  PRIMARY DLBCL OF THE CNS                                                                          3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TNFAIP3 MUTATED       3                         1     2
  TNFAIP3 WILD-TYPE    15                         0    19
D19V6, multiclass
                           clus
vv                          TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                   2                19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                   cls
clus                 0  1
  TNFAIP3 MUTATED    1  5
  TNFAIP3 WILD-TYPE 11 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED      1    5
  TNFAIP3 WILD-TYPE   11   23
                        clus
vv                       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               5                23
[1] 2 2
[1] FALSE

Clustering(20) Variable = RBMXL1 MUTATION ANALYSIS
D20V1, survival
                  sevent
clus2               0  1
  RBMXL1 MUTATED    4  0
  RBMXL1 WILD-TYPE 30  6
  RBMXL1 MUTATED RBMXL1 WILD-TYPE 
               4               36 
  RBMXL1 MUTATED RBMXL1 WILD-TYPE 
               0                6 
$`RBMXL1 MUTATED`
TCGA-FF-8042 TCGA-FF-8046 TCGA-GS-A9TU TCGA-GS-A9TV 
       31.10        24.69       128.12        24.00 

$`RBMXL1 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8047 
        8.15        14.04        18.18        35.54        31.73         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
       31.96        41.16        98.07        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       57.17        32.28        38.24        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  RBMXL1 MUTATED RBMXL1 WILD-TYPE 
           24.00             0.03 
  RBMXL1 MUTATED RBMXL1 WILD-TYPE 
          128.12           111.58 
  RBMXL1 MUTATED RBMXL1 WILD-TYPE 
          27.895           25.530 
[1] "24.0 - 128.1 (27.9)" "0.0 - 111.6 (25.5)" 
[1] "hr="     "8.1e+07"
D20V2, continuous
D20V3, binary
                  cls
clus                0  1
  RBMXL1 MUTATED    2  2
  RBMXL1 WILD-TYPE 22 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBMXL1 MUTATED      2    2
  RBMXL1 WILD-TYPE   22   14
        clus
vv       RBMXL1 MUTATED RBMXL1 WILD-TYPE
  FEMALE              2               22
  MALE                2               14
[1] 2 2
[1] FALSE
D20V4, binary
                  cls
clus                0  1
  RBMXL1 MUTATED    2  2
  RBMXL1 WILD-TYPE 31  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBMXL1 MUTATED      2    2
  RBMXL1 WILD-TYPE   31    4
     clus
vv    RBMXL1 MUTATED RBMXL1 WILD-TYPE
  NO               2               31
  YES              2                4
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  RBMXL1 MUTATED                                                                                   3
  RBMXL1 WILD-TYPE                                                                                30
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  RBMXL1 MUTATED                          0                                  1
  RBMXL1 WILD-TYPE                        3                                  3
D20V5, multiclass
                                                                                   clus
vv                                                                                  RBMXL1 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              3
  PRIMARY DLBCL OF THE CNS                                                                       0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             1
                                                                                   clus
vv                                                                                  RBMXL1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               30
  PRIMARY DLBCL OF THE CNS                                                                         3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBMXL1 MUTATED       2                         0     2
  RBMXL1 WILD-TYPE    16                         1    19
D20V6, multiclass
                           clus
vv                          RBMXL1 MUTATED RBMXL1 WILD-TYPE
  ASIAN                                  2               16
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  2               19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                  cls
clus                0  1
  RBMXL1 MUTATED    2  2
  RBMXL1 WILD-TYPE 10 26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBMXL1 MUTATED      2    2
  RBMXL1 WILD-TYPE   10   26
                        clus
vv                       RBMXL1 MUTATED RBMXL1 WILD-TYPE
  HISPANIC OR LATINO                  2               10
  NOT HISPANIC OR LATINO              2               26
[1] 2 2
[1] FALSE

Clustering(21) Variable = CCDC66 MUTATION ANALYSIS
D21V1, survival
                  sevent
clus2               0  1
  CCDC66 MUTATED    2  2
  CCDC66 WILD-TYPE 32  4
  CCDC66 MUTATED CCDC66 WILD-TYPE 
               4               36 
  CCDC66 MUTATED CCDC66 WILD-TYPE 
               2                4 
$`CCDC66 MUTATED`
TCGA-FA-A6HN TCGA-FA-A6HO TCGA-G8-6324 TCGA-GR-7353 
        1.91        24.62        41.16        98.07 

$`CCDC66 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34         4.34        23.28        23.64         8.15        14.04 
TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       18.18        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       31.96        51.98        42.71        43.86        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  CCDC66 MUTATED CCDC66 WILD-TYPE 
            1.91             0.03 
  CCDC66 MUTATED CCDC66 WILD-TYPE 
           98.07           128.12 
  CCDC66 MUTATED CCDC66 WILD-TYPE 
           32.89            25.53 
[1] "1.9 - 98.1 (32.9)"  "0.0 - 128.1 (25.5)"
[1] "hr=" "4"  
D21V2, continuous
D21V3, binary
                  cls
clus                0  1
  CCDC66 MUTATED    2  2
  CCDC66 WILD-TYPE 22 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC66 MUTATED      2    2
  CCDC66 WILD-TYPE   22   14
        clus
vv       CCDC66 MUTATED CCDC66 WILD-TYPE
  FEMALE              2               22
  MALE                2               14
[1] 2 2
[1] FALSE
D21V4, binary
                  cls
clus                0  1
  CCDC66 MUTATED    4  0
  CCDC66 WILD-TYPE 29  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC66 MUTATED      4    0
  CCDC66 WILD-TYPE   29    6
     clus
vv    CCDC66 MUTATED CCDC66 WILD-TYPE
  NO               4               29
  YES              0                6
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  CCDC66 MUTATED                                                                                   4
  CCDC66 WILD-TYPE                                                                                29
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  CCDC66 MUTATED                          0                                  0
  CCDC66 WILD-TYPE                        3                                  4
D21V5, multiclass
                                                                                   clus
vv                                                                                  CCDC66 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              4
  PRIMARY DLBCL OF THE CNS                                                                       0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             0
                                                                                   clus
vv                                                                                  CCDC66 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               29
  PRIMARY DLBCL OF THE CNS                                                                         3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC66 MUTATED       2                         1     1
  CCDC66 WILD-TYPE    16                         0    20
D21V6, multiclass
                           clus
vv                          CCDC66 MUTATED CCDC66 WILD-TYPE
  ASIAN                                  2               16
  BLACK OR AFRICAN AMERICAN              1                0
  WHITE                                  1               20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                  cls
clus                0  1
  CCDC66 MUTATED    0  4
  CCDC66 WILD-TYPE 12 24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC66 MUTATED      0    4
  CCDC66 WILD-TYPE   12   24
                        clus
vv                       CCDC66 MUTATED CCDC66 WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              4               24
[1] 2 2
[1] FALSE

Clustering(22) Variable = NOTCH2 MUTATION ANALYSIS
D22V1, survival
                  sevent
clus2               0  1
  NOTCH2 MUTATED    6  1
  NOTCH2 WILD-TYPE 28  5
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
               7               33 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
               1                5 
$`NOTCH2 MUTATED`
TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-A4D5 TCGA-GR-A4D9 
        4.34         1.91        12.66        31.96        42.71        57.17 
TCGA-RQ-AAAT 
        0.56 

$`NOTCH2 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34        23.28        24.62        23.64         8.15        14.04 
TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       18.18        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-G8-6324 
       27.35        22.32         9.80        10.29        26.01        41.16 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU 
       98.07        51.98        43.86        32.28        38.24       128.12 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 
       24.00        53.16        45.14       109.58        25.15       111.58 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
       12.85        25.91         0.03 

  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
            0.56             0.03 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
           57.17           128.12 
  NOTCH2 MUTATED NOTCH2 WILD-TYPE 
           12.66            25.91 
[1] "0.6 - 57.2 (12.7)"  "0.0 - 128.1 (25.9)"
[1] "hr=" "1.3"
D22V2, continuous
D22V3, binary
                  cls
clus                0  1
  NOTCH2 MUTATED    4  3
  NOTCH2 WILD-TYPE 20 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      4    3
  NOTCH2 WILD-TYPE   20   13
        clus
vv       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  FEMALE              4               20
  MALE                3               13
[1] 2 2
[1] FALSE
D22V4, binary
                  cls
clus                0  1
  NOTCH2 MUTATED    7  0
  NOTCH2 WILD-TYPE 26  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      7    0
  NOTCH2 WILD-TYPE   26    6
     clus
vv    NOTCH2 MUTATED NOTCH2 WILD-TYPE
  NO               7               26
  YES              0                6
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  NOTCH2 MUTATED                                                                                   6
  NOTCH2 WILD-TYPE                                                                                27
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  NOTCH2 MUTATED                          1                                  0
  NOTCH2 WILD-TYPE                        2                                  4
D22V5, multiclass
                                                                                   clus
vv                                                                                  NOTCH2 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              6
  PRIMARY DLBCL OF THE CNS                                                                       1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             0
                                                                                   clus
vv                                                                                  NOTCH2 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               27
  PRIMARY DLBCL OF THE CNS                                                                         2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NOTCH2 MUTATED       2                         0     5
  NOTCH2 WILD-TYPE    16                         1    16
D22V6, multiclass
                           clus
vv                          NOTCH2 MUTATED NOTCH2 WILD-TYPE
  ASIAN                                  2               16
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  5               16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                  cls
clus                0  1
  NOTCH2 MUTATED    1  6
  NOTCH2 WILD-TYPE 11 22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NOTCH2 MUTATED      1    6
  NOTCH2 WILD-TYPE   11   22
                        clus
vv                       NOTCH2 MUTATED NOTCH2 WILD-TYPE
  HISPANIC OR LATINO                  1               11
  NOT HISPANIC OR LATINO              6               22
[1] 2 2
[1] FALSE

Clustering(23) Variable = PCMTD1 MUTATION ANALYSIS
D23V1, survival
                  sevent
clus2               0  1
  PCMTD1 MUTATED    5  1
  PCMTD1 WILD-TYPE 29  5
  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
               6               34 
  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
               1                5 
$`PCMTD1 MUTATED`
TCGA-FF-8042 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-GS-A9TV TCGA-RQ-A68N 
       31.10        22.32        31.96        41.16        24.00        25.91 

$`PCMTD1 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 
        8.15        14.04        18.18        35.54        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
        4.14        27.35         9.80        10.29        26.01        12.66 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       98.07        51.98        42.71        43.86        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
       38.24       128.12        53.16        45.14       109.58        25.15 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB TCGA-RQ-AAAT 
      111.58        12.85         0.03         0.56 

  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
           22.32             0.03 
  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
           41.16           128.12 
  PCMTD1 MUTATED PCMTD1 WILD-TYPE 
          28.505           24.920 
[1] "22.3 - 41.2 (28.5)" "0.0 - 128.1 (24.9)"
[1] "hr=" "1"  
D23V2, continuous
D23V3, binary
                  cls
clus                0  1
  PCMTD1 MUTATED    5  1
  PCMTD1 WILD-TYPE 19 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCMTD1 MUTATED      5    1
  PCMTD1 WILD-TYPE   19   15
        clus
vv       PCMTD1 MUTATED PCMTD1 WILD-TYPE
  FEMALE              5               19
  MALE                1               15
[1] 2 2
[1] FALSE
D23V4, binary
                  cls
clus                0  1
  PCMTD1 MUTATED    5  1
  PCMTD1 WILD-TYPE 28  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCMTD1 MUTATED      5    1
  PCMTD1 WILD-TYPE   28    5
     clus
vv    PCMTD1 MUTATED PCMTD1 WILD-TYPE
  NO               5               28
  YES              1                5
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  PCMTD1 MUTATED                                                                                   4
  PCMTD1 WILD-TYPE                                                                                29
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  PCMTD1 MUTATED                          1                                  1
  PCMTD1 WILD-TYPE                        2                                  3
D23V5, multiclass
                                                                                   clus
vv                                                                                  PCMTD1 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              4
  PRIMARY DLBCL OF THE CNS                                                                       1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             1
                                                                                   clus
vv                                                                                  PCMTD1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               29
  PRIMARY DLBCL OF THE CNS                                                                         2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PCMTD1 MUTATED       2                         1     3
  PCMTD1 WILD-TYPE    16                         0    18
D23V6, multiclass
                           clus
vv                          PCMTD1 MUTATED PCMTD1 WILD-TYPE
  ASIAN                                  2               16
  BLACK OR AFRICAN AMERICAN              1                0
  WHITE                                  3               18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                  cls
clus                0  1
  PCMTD1 MUTATED    2  4
  PCMTD1 WILD-TYPE 10 24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCMTD1 MUTATED      2    4
  PCMTD1 WILD-TYPE   10   24
                        clus
vv                       PCMTD1 MUTATED PCMTD1 WILD-TYPE
  HISPANIC OR LATINO                  2               10
  NOT HISPANIC OR LATINO              4               24
[1] 2 2
[1] FALSE

Clustering(24) Variable = FAM120B MUTATION ANALYSIS
D24V1, survival
                   sevent
clus2                0  1
  FAM120B MUTATED    5  0
  FAM120B WILD-TYPE 29  6
  FAM120B MUTATED FAM120B WILD-TYPE 
                5                35 
  FAM120B MUTATED FAM120B WILD-TYPE 
                0                 6 
$`FAM120B MUTATED`
TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-A7CX TCGA-GR-A4D6 TCGA-GR-A4D9 
       31.10        24.69        12.66        43.86        57.17 

$`FAM120B WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8047 
        8.15        14.04        18.18        35.54        31.73         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FM-8000 
       27.35        22.32         9.80        10.29        26.01        31.96 
TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GS-A9TQ TCGA-GS-A9TT 
       41.16        98.07        51.98        42.71        32.28        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
      128.12        24.00        53.16        45.14       109.58        25.15 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
      111.58        12.85        25.91         0.03         0.56 

  FAM120B MUTATED FAM120B WILD-TYPE 
            12.66              0.03 
  FAM120B MUTATED FAM120B WILD-TYPE 
            57.17            128.12 
  FAM120B MUTATED FAM120B WILD-TYPE 
            31.10             25.15 
[1] "12.7 - 57.2 (31.1)" "0.0 - 128.1 (25.1)"
[1] "hr="     "2.3e+08"
D24V2, continuous
D24V3, binary
                   cls
clus                 0  1
  FAM120B MUTATED    3  2
  FAM120B WILD-TYPE 21 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM120B MUTATED      3    2
  FAM120B WILD-TYPE   21   14
        clus
vv       FAM120B MUTATED FAM120B WILD-TYPE
  FEMALE               3                21
  MALE                 2                14
[1] 2 2
[1] FALSE
D24V4, binary
                   cls
clus                 0  1
  FAM120B MUTATED    5  0
  FAM120B WILD-TYPE 28  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM120B MUTATED      5    0
  FAM120B WILD-TYPE   28    6
     clus
vv    FAM120B MUTATED FAM120B WILD-TYPE
  NO                5                28
  YES               0                 6
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  FAM120B MUTATED                                                                                   5
  FAM120B WILD-TYPE                                                                                28
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  FAM120B MUTATED                          0                                  0
  FAM120B WILD-TYPE                        3                                  4
D24V5, multiclass
                                                                                   clus
vv                                                                                  FAM120B MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               5
  PRIMARY DLBCL OF THE CNS                                                                        0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              0
                                                                                   clus
vv                                                                                  FAM120B WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                28
  PRIMARY DLBCL OF THE CNS                                                                          3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM120B MUTATED       4                         0     1
  FAM120B WILD-TYPE    14                         1    20
D24V6, multiclass
                           clus
vv                          FAM120B MUTATED FAM120B WILD-TYPE
  ASIAN                                   4                14
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   1                20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                   cls
clus                 0  1
  FAM120B MUTATED    0  5
  FAM120B WILD-TYPE 12 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM120B MUTATED      0    5
  FAM120B WILD-TYPE   12   23
                        clus
vv                       FAM120B MUTATED FAM120B WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               5                23
[1] 2 2
[1] FALSE

Clustering(25) Variable = SMARCA2 MUTATION ANALYSIS
D25V1, survival
                   sevent
clus2                0  1
  SMARCA2 MUTATED    4  0
  SMARCA2 WILD-TYPE 30  6
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
                4                36 
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
                0                 6 
$`SMARCA2 MUTATED`
TCGA-FF-8047 TCGA-FF-8062 TCGA-GR-A4D4 TCGA-GR-A4D5 
        4.14        22.32        51.98        42.71 

$`SMARCA2 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       24.69        27.35         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       31.96        41.16        98.07        43.86        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
             4.14              0.03 
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
            51.98            128.12 
  SMARCA2 MUTATED SMARCA2 WILD-TYPE 
           32.515            25.530 
[1] "4.1 - 52.0 (32.5)"  "0.0 - 128.1 (25.5)"
[1] "hr="   "8e+07"
D25V2, continuous
D25V3, binary
                   cls
clus                 0  1
  SMARCA2 MUTATED    4  0
  SMARCA2 WILD-TYPE 20 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA2 MUTATED      4    0
  SMARCA2 WILD-TYPE   20   16
        clus
vv       SMARCA2 MUTATED SMARCA2 WILD-TYPE
  FEMALE               4                20
  MALE                 0                16
[1] 2 2
[1] FALSE
D25V4, binary
                   cls
clus                 0  1
  SMARCA2 MUTATED    4  0
  SMARCA2 WILD-TYPE 29  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA2 MUTATED      4    0
  SMARCA2 WILD-TYPE   29    6
     clus
vv    SMARCA2 MUTATED SMARCA2 WILD-TYPE
  NO                4                29
  YES               0                 6
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  SMARCA2 MUTATED                                                                                   4
  SMARCA2 WILD-TYPE                                                                                29
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  SMARCA2 MUTATED                          0                                  0
  SMARCA2 WILD-TYPE                        3                                  4
D25V5, multiclass
                                                                                   clus
vv                                                                                  SMARCA2 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               4
  PRIMARY DLBCL OF THE CNS                                                                        0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              0
                                                                                   clus
vv                                                                                  SMARCA2 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                29
  PRIMARY DLBCL OF THE CNS                                                                          3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMARCA2 MUTATED       2                         0     2
  SMARCA2 WILD-TYPE    16                         1    19
D25V6, multiclass
                           clus
vv                          SMARCA2 MUTATED SMARCA2 WILD-TYPE
  ASIAN                                   2                16
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   2                19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                   cls
clus                 0  1
  SMARCA2 MUTATED    0  4
  SMARCA2 WILD-TYPE 12 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA2 MUTATED      0    4
  SMARCA2 WILD-TYPE   12   24
                        clus
vv                       SMARCA2 MUTATED SMARCA2 WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               4                24
[1] 2 2
[1] FALSE

Clustering(26) Variable = C11ORF40 MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  C11ORF40 MUTATED    3  1
  C11ORF40 WILD-TYPE 31  5
  C11ORF40 MUTATED C11ORF40 WILD-TYPE 
                 4                 36 
  C11ORF40 MUTATED C11ORF40 WILD-TYPE 
                 1                  5 
$`C11ORF40 MUTATED`
TCGA-FA-A82F TCGA-FF-A7CQ TCGA-FF-A7CW TCGA-G8-6324 
       14.04         9.80        26.01        41.16 

$`C11ORF40 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
        8.15        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 
        4.14        27.35        22.32        10.29        12.66        31.96 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       98.07        51.98        42.71        43.86        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  C11ORF40 MUTATED C11ORF40 WILD-TYPE 
              9.80               0.03 
  C11ORF40 MUTATED C11ORF40 WILD-TYPE 
             41.16             128.12 
  C11ORF40 MUTATED C11ORF40 WILD-TYPE 
            20.025             25.530 
[1] "9.8 - 41.2 (20.0)"  "0.0 - 128.1 (25.5)"
[1] "hr=" "1.9"
D26V2, continuous
D26V3, binary
                    cls
clus                  0  1
  C11ORF40 MUTATED    2  2
  C11ORF40 WILD-TYPE 22 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF40 MUTATED      2    2
  C11ORF40 WILD-TYPE   22   14
        clus
vv       C11ORF40 MUTATED C11ORF40 WILD-TYPE
  FEMALE                2                 22
  MALE                  2                 14
[1] 2 2
[1] FALSE
D26V4, binary
                    cls
clus                  0  1
  C11ORF40 MUTATED    4  0
  C11ORF40 WILD-TYPE 29  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF40 MUTATED      4    0
  C11ORF40 WILD-TYPE   29    6
     clus
vv    C11ORF40 MUTATED C11ORF40 WILD-TYPE
  NO                 4                 29
  YES                0                  6
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  C11ORF40 MUTATED                                                                                   4
  C11ORF40 WILD-TYPE                                                                                29
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  C11ORF40 MUTATED                          0
  C11ORF40 WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  C11ORF40 MUTATED                                    0
  C11ORF40 WILD-TYPE                                  4
D26V5, multiclass
                                                                                   clus
vv                                                                                  C11ORF40 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                4
  PRIMARY DLBCL OF THE CNS                                                                         0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               0
                                                                                   clus
vv                                                                                  C11ORF40 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 29
  PRIMARY DLBCL OF THE CNS                                                                           3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C11ORF40 MUTATED       3                         1     0
  C11ORF40 WILD-TYPE    15                         0    21
D26V6, multiclass
                           clus
vv                          C11ORF40 MUTATED C11ORF40 WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                    0                 21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                    cls
clus                  0  1
  C11ORF40 MUTATED    0  4
  C11ORF40 WILD-TYPE 12 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF40 MUTATED      0    4
  C11ORF40 WILD-TYPE   12   24
                        clus
vv                       C11ORF40 MUTATED C11ORF40 WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                4                 24
[1] 2 2
[1] FALSE

Clustering(27) Variable = ZSCAN5A MUTATION ANALYSIS
D27V1, survival
                   sevent
clus2                0  1
  ZSCAN5A MUTATED    3  0
  ZSCAN5A WILD-TYPE 31  6
  ZSCAN5A MUTATED ZSCAN5A WILD-TYPE 
                3                37 
  ZSCAN5A MUTATED ZSCAN5A WILD-TYPE 
                0                 6 
$`ZSCAN5A MUTATED`
TCGA-GR-7353 TCGA-GR-A4D6 TCGA-GS-A9U3 
       98.07        43.86       111.58 

$`ZSCAN5A WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       24.69         4.14        27.35        22.32         9.80        10.29 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-A4D4 TCGA-GR-A4D5 
       26.01        12.66        31.96        41.16        51.98        42.71 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       57.17        32.28        38.24       128.12        24.00        53.16 
TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
       45.14       109.58        25.15        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  ZSCAN5A MUTATED ZSCAN5A WILD-TYPE 
            43.86              0.03 
  ZSCAN5A MUTATED ZSCAN5A WILD-TYPE 
           111.58            128.12 
  ZSCAN5A MUTATED ZSCAN5A WILD-TYPE 
            98.07             24.69 
[1] "43.9 - 111.6 (98.1)" "0.0 - 128.1 (24.7)" 
[1] "hr="     "8.8e+07"
D27V2, continuous
D27V3, binary
                   cls
clus                 0  1
  ZSCAN5A MUTATED    2  1
  ZSCAN5A WILD-TYPE 22 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZSCAN5A MUTATED      2    1
  ZSCAN5A WILD-TYPE   22   15
        clus
vv       ZSCAN5A MUTATED ZSCAN5A WILD-TYPE
  FEMALE               2                22
  MALE                 1                15
[1] 2 2
[1] FALSE
D27V4, binary
                   cls
clus                 0  1
  ZSCAN5A MUTATED    3  0
  ZSCAN5A WILD-TYPE 30  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZSCAN5A MUTATED      3    0
  ZSCAN5A WILD-TYPE   30    6
     clus
vv    ZSCAN5A MUTATED ZSCAN5A WILD-TYPE
  NO                3                30
  YES               0                 6
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  ZSCAN5A MUTATED                                                                                   3
  ZSCAN5A WILD-TYPE                                                                                30
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  ZSCAN5A MUTATED                          0                                  0
  ZSCAN5A WILD-TYPE                        3                                  4
D27V5, multiclass
                                                                                   clus
vv                                                                                  ZSCAN5A MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               3
  PRIMARY DLBCL OF THE CNS                                                                        0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              0
                                                                                   clus
vv                                                                                  ZSCAN5A WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                30
  PRIMARY DLBCL OF THE CNS                                                                          3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZSCAN5A MUTATED       1                         0     2
  ZSCAN5A WILD-TYPE    17                         1    19
D27V6, multiclass
                           clus
vv                          ZSCAN5A MUTATED ZSCAN5A WILD-TYPE
  ASIAN                                   1                17
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   2                19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                   cls
clus                 0  1
  ZSCAN5A MUTATED    1  2
  ZSCAN5A WILD-TYPE 11 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZSCAN5A MUTATED      1    2
  ZSCAN5A WILD-TYPE   11   26
                        clus
vv                       ZSCAN5A MUTATED ZSCAN5A WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               2                26
[1] 2 2
[1] FALSE

Clustering(28) Variable = KRTAP4-5 MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  KRTAP4-5 MUTATED    3  1
  KRTAP4-5 WILD-TYPE 31  5
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 4                 36 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
                 1                  5 
$`KRTAP4-5 MUTATED`
TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-RQ-A6JB 
       41.16        98.07        51.98         0.03 

$`KRTAP4-5 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       24.69         4.14        27.35        22.32         9.80        10.29 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       26.01        12.66        31.96        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       32.28        38.24       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-AAAT 
      109.58        25.15       111.58        12.85        25.91         0.56 

  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
              0.03               0.56 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
             98.07             128.12 
  KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE 
             46.57              24.92 
[1] "0.0 - 98.1 (46.6)"  "0.6 - 128.1 (24.9)"
[1] "hr=" "1.4"
D28V2, continuous
D28V3, binary
                    cls
clus                  0  1
  KRTAP4-5 MUTATED    3  1
  KRTAP4-5 WILD-TYPE 21 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-5 MUTATED      3    1
  KRTAP4-5 WILD-TYPE   21   15
        clus
vv       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  FEMALE                3                 21
  MALE                  1                 15
[1] 2 2
[1] FALSE
D28V4, binary
                    cls
clus                  0  1
  KRTAP4-5 MUTATED    3  0
  KRTAP4-5 WILD-TYPE 30  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-5 MUTATED      3    0
  KRTAP4-5 WILD-TYPE   30    6
     clus
vv    KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  NO                 3                 30
  YES                0                  6
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  KRTAP4-5 MUTATED                                                                                   3
  KRTAP4-5 WILD-TYPE                                                                                30
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  KRTAP4-5 MUTATED                          1
  KRTAP4-5 WILD-TYPE                        2
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  KRTAP4-5 MUTATED                                    0
  KRTAP4-5 WILD-TYPE                                  4
D28V5, multiclass
                                                                                   clus
vv                                                                                  KRTAP4-5 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                3
  PRIMARY DLBCL OF THE CNS                                                                         1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               0
                                                                                   clus
vv                                                                                  KRTAP4-5 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 30
  PRIMARY DLBCL OF THE CNS                                                                           2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRTAP4-5 MUTATED       0                         1     3
  KRTAP4-5 WILD-TYPE    18                         0    18
D28V6, multiclass
                           clus
vv                          KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  ASIAN                                    0                 18
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                    3                 18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                    cls
clus                  0  1
  KRTAP4-5 MUTATED    0  4
  KRTAP4-5 WILD-TYPE 12 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-5 MUTATED      0    4
  KRTAP4-5 WILD-TYPE   12   24
                        clus
vv                       KRTAP4-5 MUTATED KRTAP4-5 WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                4                 24
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEFA1 MUTATION ANALYSIS
D29V1, survival
                 sevent
clus2              0  1
  DEFA1 MUTATED    2  2
  DEFA1 WILD-TYPE 32  4
  DEFA1 MUTATED DEFA1 WILD-TYPE 
              4              36 
  DEFA1 MUTATED DEFA1 WILD-TYPE 
              2               4 
$`DEFA1 MUTATED`
TCGA-FF-A7CR TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-7353 
       10.29        31.96        41.16        98.07 

$`DEFA1 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CW 
       24.69         4.14        27.35        22.32         9.80        26.01 
TCGA-FF-A7CX TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       12.66        51.98        42.71        43.86        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  DEFA1 MUTATED DEFA1 WILD-TYPE 
          10.29            0.03 
  DEFA1 MUTATED DEFA1 WILD-TYPE 
          98.07          128.12 
  DEFA1 MUTATED DEFA1 WILD-TYPE 
          36.56           24.92 
[1] "10.3 - 98.1 (36.6)" "0.0 - 128.1 (24.9)"
[1] "hr=" "3.6"
D29V2, continuous
D29V3, binary
                 cls
clus               0  1
  DEFA1 MUTATED    2  2
  DEFA1 WILD-TYPE 22 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DEFA1 MUTATED      2    2
  DEFA1 WILD-TYPE   22   14
        clus
vv       DEFA1 MUTATED DEFA1 WILD-TYPE
  FEMALE             2              22
  MALE               2              14
[1] 2 2
[1] FALSE
D29V4, binary
                 cls
clus               0  1
  DEFA1 MUTATED    4  0
  DEFA1 WILD-TYPE 29  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DEFA1 MUTATED      4    0
  DEFA1 WILD-TYPE   29    6
     clus
vv    DEFA1 MUTATED DEFA1 WILD-TYPE
  NO              4              29
  YES             0               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEFA1 MUTATED                                                                                   4
  DEFA1 WILD-TYPE                                                                                29
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEFA1 MUTATED                          0                                  0
  DEFA1 WILD-TYPE                        3                                  4
D29V5, multiclass
                                                                                   clus
vv                                                                                  DEFA1 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             4
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  DEFA1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              29
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEFA1 MUTATED       1                         1     2
  DEFA1 WILD-TYPE    17                         0    19
D29V6, multiclass
                           clus
vv                          DEFA1 MUTATED DEFA1 WILD-TYPE
  ASIAN                                 1              17
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 2              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                 cls
clus               0  1
  DEFA1 MUTATED    0  4
  DEFA1 WILD-TYPE 12 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DEFA1 MUTATED      0    4
  DEFA1 WILD-TYPE   12   24
                        clus
vv                       DEFA1 MUTATED DEFA1 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             4              24
[1] 2 2
[1] FALSE

Clustering(30) Variable = SIRPA MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2              0  1
  SIRPA MUTATED    3  2
  SIRPA WILD-TYPE 31  4
  SIRPA MUTATED SIRPA WILD-TYPE 
              5              35 
  SIRPA MUTATED SIRPA WILD-TYPE 
              2               4 
$`SIRPA MUTATED`
TCGA-FA-A6HN TCGA-FF-8041 TCGA-G8-6324 TCGA-GR-7353 TCGA-RQ-A68N 
        1.91        35.54        41.16        98.07        25.91 

$`SIRPA WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        23.28        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       14.04        18.18        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       31.96        51.98        42.71        43.86        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85         0.03         0.56 

  SIRPA MUTATED SIRPA WILD-TYPE 
           1.91            0.03 
  SIRPA MUTATED SIRPA WILD-TYPE 
          98.07          128.12 
  SIRPA MUTATED SIRPA WILD-TYPE 
          35.54           24.69 
[1] "1.9 - 98.1 (35.5)"  "0.0 - 128.1 (24.7)"
[1] "hr=" "3.1"
D30V2, continuous
D30V3, binary
                 cls
clus               0  1
  SIRPA MUTATED    2  3
  SIRPA WILD-TYPE 22 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIRPA MUTATED      2    3
  SIRPA WILD-TYPE   22   13
        clus
vv       SIRPA MUTATED SIRPA WILD-TYPE
  FEMALE             2              22
  MALE               3              13
[1] 2 2
[1] FALSE
D30V4, binary
                 cls
clus               0  1
  SIRPA MUTATED    5  0
  SIRPA WILD-TYPE 28  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIRPA MUTATED      5    0
  SIRPA WILD-TYPE   28    6
     clus
vv    SIRPA MUTATED SIRPA WILD-TYPE
  NO              5              28
  YES             0               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  SIRPA MUTATED                                                                                   3
  SIRPA WILD-TYPE                                                                                30
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  SIRPA MUTATED                          1                                  1
  SIRPA WILD-TYPE                        2                                  3
D30V5, multiclass
                                                                                   clus
vv                                                                                  SIRPA MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             3
  PRIMARY DLBCL OF THE CNS                                                                      1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            1
                                                                                   clus
vv                                                                                  SIRPA WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              30
  PRIMARY DLBCL OF THE CNS                                                                        2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SIRPA MUTATED       2                         1     2
  SIRPA WILD-TYPE    16                         0    19
D30V6, multiclass
                           clus
vv                          SIRPA MUTATED SIRPA WILD-TYPE
  ASIAN                                 2              16
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 2              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                 cls
clus               0  1
  SIRPA MUTATED    1  4
  SIRPA WILD-TYPE 11 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIRPA MUTATED      1    4
  SIRPA WILD-TYPE   11   24
                        clus
vv                       SIRPA MUTATED SIRPA WILD-TYPE
  HISPANIC OR LATINO                 1              11
  NOT HISPANIC OR LATINO             4              24
[1] 2 2
[1] FALSE

Clustering(31) Variable = TMPRSS13 MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  TMPRSS13 MUTATED    3  0
  TMPRSS13 WILD-TYPE 31  6
  TMPRSS13 MUTATED TMPRSS13 WILD-TYPE 
                 3                 37 
  TMPRSS13 MUTATED TMPRSS13 WILD-TYPE 
                 0                  6 
$`TMPRSS13 MUTATED`
TCGA-FA-8693 TCGA-FF-8047 TCGA-GR-7353 
        4.34         4.14        98.07 

$`TMPRSS13 WILD-TYPE`
TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34        23.28         1.91        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       31.96        41.16        51.98        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       32.28        38.24       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  TMPRSS13 MUTATED TMPRSS13 WILD-TYPE 
              4.14               0.03 
  TMPRSS13 MUTATED TMPRSS13 WILD-TYPE 
             98.07             128.12 
  TMPRSS13 MUTATED TMPRSS13 WILD-TYPE 
              4.34              25.91 
[1] "4.1 - 98.1 (4.3)"   "0.0 - 128.1 (25.9)"
[1] "hr="     "7.3e+07"
D31V2, continuous
D31V3, binary
                    cls
clus                  0  1
  TMPRSS13 MUTATED    1  2
  TMPRSS13 WILD-TYPE 23 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMPRSS13 MUTATED      1    2
  TMPRSS13 WILD-TYPE   23   14
        clus
vv       TMPRSS13 MUTATED TMPRSS13 WILD-TYPE
  FEMALE                1                 23
  MALE                  2                 14
[1] 2 2
[1] FALSE
D31V4, binary
                    cls
clus                  0  1
  TMPRSS13 MUTATED    3  0
  TMPRSS13 WILD-TYPE 30  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMPRSS13 MUTATED      3    0
  TMPRSS13 WILD-TYPE   30    6
     clus
vv    TMPRSS13 MUTATED TMPRSS13 WILD-TYPE
  NO                 3                 30
  YES                0                  6
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  TMPRSS13 MUTATED                                                                                   3
  TMPRSS13 WILD-TYPE                                                                                30
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  TMPRSS13 MUTATED                          0
  TMPRSS13 WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  TMPRSS13 MUTATED                                    0
  TMPRSS13 WILD-TYPE                                  4
D31V5, multiclass
                                                                                   clus
vv                                                                                  TMPRSS13 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                3
  PRIMARY DLBCL OF THE CNS                                                                         0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               0
                                                                                   clus
vv                                                                                  TMPRSS13 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 30
  PRIMARY DLBCL OF THE CNS                                                                           3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMPRSS13 MUTATED       1                         0     2
  TMPRSS13 WILD-TYPE    17                         1    19
D31V6, multiclass
                           clus
vv                          TMPRSS13 MUTATED TMPRSS13 WILD-TYPE
  ASIAN                                    1                 17
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                    cls
clus                  0  1
  TMPRSS13 MUTATED    0  3
  TMPRSS13 WILD-TYPE 12 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMPRSS13 MUTATED      0    3
  TMPRSS13 WILD-TYPE   12   25
                        clus
vv                       TMPRSS13 MUTATED TMPRSS13 WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                3                 25
[1] 2 2
[1] FALSE

Clustering(32) Variable = CYP2A6 MUTATION ANALYSIS
D32V1, survival
                  sevent
clus2               0  1
  CYP2A6 MUTATED    4  0
  CYP2A6 WILD-TYPE 30  6
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
               4               36 
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
               0                6 
$`CYP2A6 MUTATED`
TCGA-FF-8047 TCGA-FF-8061 TCGA-GR-7353 TCGA-GS-A9TU 
        4.14        27.35        98.07       128.12 

$`CYP2A6 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       24.69        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       31.96        41.16        51.98        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       32.28        38.24        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
            4.14             0.03 
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
          128.12           111.58 
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
           62.71            24.92 
[1] "4.1 - 128.1 (62.7)" "0.0 - 111.6 (24.9)"
[1] "hr="     "8.1e+07"
D32V2, continuous
D32V3, binary
                  cls
clus                0  1
  CYP2A6 MUTATED    1  3
  CYP2A6 WILD-TYPE 23 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2A6 MUTATED      1    3
  CYP2A6 WILD-TYPE   23   13
        clus
vv       CYP2A6 MUTATED CYP2A6 WILD-TYPE
  FEMALE              1               23
  MALE                3               13
[1] 2 2
[1] FALSE
D32V4, binary
                  cls
clus                0  1
  CYP2A6 MUTATED    3  1
  CYP2A6 WILD-TYPE 30  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2A6 MUTATED      3    1
  CYP2A6 WILD-TYPE   30    5
     clus
vv    CYP2A6 MUTATED CYP2A6 WILD-TYPE
  NO               3               30
  YES              1                5
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  CYP2A6 MUTATED                                                                                   4
  CYP2A6 WILD-TYPE                                                                                29
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  CYP2A6 MUTATED                          0                                  0
  CYP2A6 WILD-TYPE                        3                                  4
D32V5, multiclass
                                                                                   clus
vv                                                                                  CYP2A6 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              4
  PRIMARY DLBCL OF THE CNS                                                                       0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             0
                                                                                   clus
vv                                                                                  CYP2A6 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               29
  PRIMARY DLBCL OF THE CNS                                                                         3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CYP2A6 MUTATED       2                         0     2
  CYP2A6 WILD-TYPE    16                         1    19
D32V6, multiclass
                           clus
vv                          CYP2A6 MUTATED CYP2A6 WILD-TYPE
  ASIAN                                  2               16
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  2               19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                  cls
clus                0  1
  CYP2A6 MUTATED    1  3
  CYP2A6 WILD-TYPE 11 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2A6 MUTATED      1    3
  CYP2A6 WILD-TYPE   11   25
                        clus
vv                       CYP2A6 MUTATED CYP2A6 WILD-TYPE
  HISPANIC OR LATINO                  1               11
  NOT HISPANIC OR LATINO              3               25
[1] 2 2
[1] FALSE

Clustering(33) Variable = AR MUTATION ANALYSIS
D33V1, survival
              sevent
clus2           0  1
  AR MUTATED    5  2
  AR WILD-TYPE 29  4
  AR MUTATED AR WILD-TYPE 
           7           33 
  AR MUTATED AR WILD-TYPE 
           2            4 
$`AR MUTATED`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8046 TCGA-G8-6324 TCGA-GR-A4D6 TCGA-GS-A9TW 
       23.28        35.54        24.69        41.16        43.86        53.16 
TCGA-GS-A9TY 
      109.58 

$`AR WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         1.91        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 
       14.04        18.18        31.10        31.73         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT 
       98.07        51.98        42.71        57.17        32.28        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 
      128.12        24.00        45.14        25.15       111.58        12.85 
TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.91         0.03         0.56 

  AR MUTATED AR WILD-TYPE 
       23.28         0.03 
  AR MUTATED AR WILD-TYPE 
      109.58       128.12 
  AR MUTATED AR WILD-TYPE 
       41.16        24.62 
[1] "23.3 - 109.6 (41.2)" "0.0 - 128.1 (24.6)" 
[1] "hr=" "1.5"
D33V2, continuous
D33V3, binary
              cls
clus            0  1
  AR MUTATED    5  2
  AR WILD-TYPE 19 14
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      5    2
  AR WILD-TYPE   19   14
        clus
vv       AR MUTATED AR WILD-TYPE
  FEMALE          5           19
  MALE            2           14
[1] 2 2
[1] FALSE
D33V4, binary
              cls
clus            0  1
  AR MUTATED    6  1
  AR WILD-TYPE 27  5
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      6    1
  AR WILD-TYPE   27    5
     clus
vv    AR MUTATED AR WILD-TYPE
  NO           6           27
  YES          1            5
[1] 2 2
[1] FALSE
              vv
clus           DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  AR MUTATED                                                                                   5
  AR WILD-TYPE                                                                                28
              vv
clus           PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  AR MUTATED                          0                                  2
  AR WILD-TYPE                        3                                  2
D33V5, multiclass
                                                                                   clus
vv                                                                                  AR MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)          5
  PRIMARY DLBCL OF THE CNS                                                                   0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                         2
                                                                                   clus
vv                                                                                  AR WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)           28
  PRIMARY DLBCL OF THE CNS                                                                     3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                           2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AR MUTATED       4                         1     2
  AR WILD-TYPE    14                         0    19
D33V6, multiclass
                           clus
vv                          AR MUTATED AR WILD-TYPE
  ASIAN                              4           14
  BLACK OR AFRICAN AMERICAN          1            0
  WHITE                              2           19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
              cls
clus            0  1
  AR MUTATED    2  5
  AR WILD-TYPE 10 23
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      2    5
  AR WILD-TYPE   10   23
                        clus
vv                       AR MUTATED AR WILD-TYPE
  HISPANIC OR LATINO              2           10
  NOT HISPANIC OR LATINO          5           23
[1] 2 2
[1] FALSE

Clustering(34) Variable = ARHGEF5 MUTATION ANALYSIS
D34V1, survival
                   sevent
clus2                0  1
  ARHGEF5 MUTATED    2  1
  ARHGEF5 WILD-TYPE 32  5
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                3                37 
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
                1                 5 
$`ARHGEF5 MUTATED`
TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-A4D9 
       31.96        41.16        57.17 

$`ARHGEF5 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       24.69         4.14        27.35        22.32         9.80        10.29 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
       26.01        12.66        98.07        51.98        42.71        43.86 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       32.28        38.24       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
            31.96              0.03 
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
            57.17            128.12 
  ARHGEF5 MUTATED ARHGEF5 WILD-TYPE 
            41.16             24.69 
[1] "32.0 - 57.2 (41.2)" "0.0 - 128.1 (24.7)"
[1] "hr=" "1.6"
D34V2, continuous
D34V3, binary
                   cls
clus                 0  1
  ARHGEF5 MUTATED    3  0
  ARHGEF5 WILD-TYPE 21 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF5 MUTATED      3    0
  ARHGEF5 WILD-TYPE   21   16
        clus
vv       ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  FEMALE               3                21
  MALE                 0                16
[1] 2 2
[1] FALSE
D34V4, binary
                   cls
clus                 0  1
  ARHGEF5 MUTATED    3  0
  ARHGEF5 WILD-TYPE 30  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF5 MUTATED      3    0
  ARHGEF5 WILD-TYPE   30    6
     clus
vv    ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  NO                3                30
  YES               0                 6
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  ARHGEF5 MUTATED                                                                                   3
  ARHGEF5 WILD-TYPE                                                                                30
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  ARHGEF5 MUTATED                          0                                  0
  ARHGEF5 WILD-TYPE                        3                                  4
D34V5, multiclass
                                                                                   clus
vv                                                                                  ARHGEF5 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               3
  PRIMARY DLBCL OF THE CNS                                                                        0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              0
                                                                                   clus
vv                                                                                  ARHGEF5 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                30
  PRIMARY DLBCL OF THE CNS                                                                          3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARHGEF5 MUTATED       0                         1     2
  ARHGEF5 WILD-TYPE    18                         0    19
D34V6, multiclass
                           clus
vv                          ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  ASIAN                                   0                18
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                   2                19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                   cls
clus                 0  1
  ARHGEF5 MUTATED    0  3
  ARHGEF5 WILD-TYPE 12 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF5 MUTATED      0    3
  ARHGEF5 WILD-TYPE   12   25
                        clus
vv                       ARHGEF5 MUTATED ARHGEF5 WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               3                25
[1] 2 2
[1] FALSE

Clustering(35) Variable = RNF39 MUTATION ANALYSIS
D35V1, survival
                 sevent
clus2              0  1
  RNF39 MUTATED    2  1
  RNF39 WILD-TYPE 32  5
  RNF39 MUTATED RNF39 WILD-TYPE 
              3              37 
  RNF39 MUTATED RNF39 WILD-TYPE 
              1               5 
$`RNF39 MUTATED`
TCGA-G8-6324 TCGA-GR-7353 TCGA-RQ-A68N 
       41.16        98.07        25.91 

$`RNF39 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       24.69         4.14        27.35        22.32         9.80        10.29 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
       26.01        12.66        31.96        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       57.17        32.28        38.24       128.12        24.00        53.16 
TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB 
       45.14       109.58        25.15       111.58        12.85         0.03 
TCGA-RQ-AAAT 
        0.56 

  RNF39 MUTATED RNF39 WILD-TYPE 
          25.91            0.03 
  RNF39 MUTATED RNF39 WILD-TYPE 
          98.07          128.12 
  RNF39 MUTATED RNF39 WILD-TYPE 
          41.16           24.69 
[1] "25.9 - 98.1 (41.2)" "0.0 - 128.1 (24.7)"
[1] "hr=" "1.6"
D35V2, continuous
D35V3, binary
                 cls
clus               0  1
  RNF39 MUTATED    1  2
  RNF39 WILD-TYPE 23 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF39 MUTATED      1    2
  RNF39 WILD-TYPE   23   14
        clus
vv       RNF39 MUTATED RNF39 WILD-TYPE
  FEMALE             1              23
  MALE               2              14
[1] 2 2
[1] FALSE
D35V4, binary
                 cls
clus               0  1
  RNF39 MUTATED    3  0
  RNF39 WILD-TYPE 30  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF39 MUTATED      3    0
  RNF39 WILD-TYPE   30    6
     clus
vv    RNF39 MUTATED RNF39 WILD-TYPE
  NO              3              30
  YES             0               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  RNF39 MUTATED                                                                                   2
  RNF39 WILD-TYPE                                                                                31
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  RNF39 MUTATED                          1                                  0
  RNF39 WILD-TYPE                        2                                  4
D35V5, multiclass
                                                                                   clus
vv                                                                                  RNF39 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             2
  PRIMARY DLBCL OF THE CNS                                                                      1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  RNF39 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              31
  PRIMARY DLBCL OF THE CNS                                                                        2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RNF39 MUTATED       0                         1     2
  RNF39 WILD-TYPE    18                         0    19
D35V6, multiclass
                           clus
vv                          RNF39 MUTATED RNF39 WILD-TYPE
  ASIAN                                 0              18
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 2              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                 cls
clus               0  1
  RNF39 MUTATED    1  2
  RNF39 WILD-TYPE 11 26
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF39 MUTATED      1    2
  RNF39 WILD-TYPE   11   26
                        clus
vv                       RNF39 MUTATED RNF39 WILD-TYPE
  HISPANIC OR LATINO                 1              11
  NOT HISPANIC OR LATINO             2              26
[1] 2 2
[1] FALSE

Clustering(36) Variable = ABCA1 MUTATION ANALYSIS
D36V1, survival
                 sevent
clus2              0  1
  ABCA1 MUTATED    3  2
  ABCA1 WILD-TYPE 31  4
  ABCA1 MUTATED ABCA1 WILD-TYPE 
              5              35 
  ABCA1 MUTATED ABCA1 WILD-TYPE 
              2               4 
$`ABCA1 MUTATED`
TCGA-FA-A4XK TCGA-FF-A7CW TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D9 
       23.28        26.01        41.16        98.07        57.17 

$`ABCA1 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         1.91        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CX 
        4.14        27.35        22.32         9.80        10.29        12.66 
TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GS-A9TQ TCGA-GS-A9TT 
       31.96        51.98        42.71        43.86        32.28        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
      128.12        24.00        53.16        45.14       109.58        25.15 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
      111.58        12.85        25.91         0.03         0.56 

  ABCA1 MUTATED ABCA1 WILD-TYPE 
          23.28            0.03 
  ABCA1 MUTATED ABCA1 WILD-TYPE 
          98.07          128.12 
  ABCA1 MUTATED ABCA1 WILD-TYPE 
          41.16           24.69 
[1] "23.3 - 98.1 (41.2)" "0.0 - 128.1 (24.7)"
[1] "hr=" "2.3"
D36V2, continuous
D36V3, binary
                 cls
clus               0  1
  ABCA1 MUTATED    2  3
  ABCA1 WILD-TYPE 22 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA1 MUTATED      2    3
  ABCA1 WILD-TYPE   22   13
        clus
vv       ABCA1 MUTATED ABCA1 WILD-TYPE
  FEMALE             2              22
  MALE               3              13
[1] 2 2
[1] FALSE
D36V4, binary
                 cls
clus               0  1
  ABCA1 MUTATED    5  0
  ABCA1 WILD-TYPE 28  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA1 MUTATED      5    0
  ABCA1 WILD-TYPE   28    6
     clus
vv    ABCA1 MUTATED ABCA1 WILD-TYPE
  NO              5              28
  YES             0               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  ABCA1 MUTATED                                                                                   5
  ABCA1 WILD-TYPE                                                                                28
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  ABCA1 MUTATED                          0                                  0
  ABCA1 WILD-TYPE                        3                                  4
D36V5, multiclass
                                                                                   clus
vv                                                                                  ABCA1 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             5
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  ABCA1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              28
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ABCA1 MUTATED       2                         1     2
  ABCA1 WILD-TYPE    16                         0    19
D36V6, multiclass
                           clus
vv                          ABCA1 MUTATED ABCA1 WILD-TYPE
  ASIAN                                 2              16
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 2              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                 cls
clus               0  1
  ABCA1 MUTATED    0  5
  ABCA1 WILD-TYPE 12 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCA1 MUTATED      0    5
  ABCA1 WILD-TYPE   12   23
                        clus
vv                       ABCA1 MUTATED ABCA1 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             5              23
[1] 2 2
[1] FALSE

Clustering(37) Variable = CS MUTATION ANALYSIS
D37V1, survival
              sevent
clus2           0  1
  CS MUTATED    2  1
  CS WILD-TYPE 32  5
  CS MUTATED CS WILD-TYPE 
           3           37 
  CS MUTATED CS WILD-TYPE 
           1            5 
$`CS MUTATED`
TCGA-G8-6324 TCGA-GR-A4D4 TCGA-GS-A9TV 
       41.16        51.98        24.00 

$`CS WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       24.69         4.14        27.35        22.32         9.80        10.29 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 
       26.01        12.66        31.96        98.07        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TW TCGA-GS-A9TX 
       57.17        32.28        38.24       128.12        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  CS MUTATED CS WILD-TYPE 
       24.00         0.03 
  CS MUTATED CS WILD-TYPE 
       51.98       128.12 
  CS MUTATED CS WILD-TYPE 
       41.16        25.15 
[1] "24.0 - 52.0 (41.2)" "0.0 - 128.1 (25.1)"
[1] "hr=" "1.6"
D37V2, continuous
D37V3, binary
              cls
clus            0  1
  CS MUTATED    3  0
  CS WILD-TYPE 21 16
[1] "tbl2"
              cls
clus           [,1] [,2]
  CS MUTATED      3    0
  CS WILD-TYPE   21   16
        clus
vv       CS MUTATED CS WILD-TYPE
  FEMALE          3           21
  MALE            0           16
[1] 2 2
[1] FALSE
D37V4, binary
              cls
clus            0  1
  CS MUTATED    2  1
  CS WILD-TYPE 31  5
[1] "tbl2"
              cls
clus           [,1] [,2]
  CS MUTATED      2    1
  CS WILD-TYPE   31    5
     clus
vv    CS MUTATED CS WILD-TYPE
  NO           2           31
  YES          1            5
[1] 2 2
[1] FALSE
              vv
clus           DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  CS MUTATED                                                                                   2
  CS WILD-TYPE                                                                                31
              vv
clus           PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  CS MUTATED                          0                                  1
  CS WILD-TYPE                        3                                  3
D37V5, multiclass
                                                                                   clus
vv                                                                                  CS MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)          2
  PRIMARY DLBCL OF THE CNS                                                                   0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                         1
                                                                                   clus
vv                                                                                  CS WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)           31
  PRIMARY DLBCL OF THE CNS                                                                     3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                           3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CS MUTATED       0                         1     2
  CS WILD-TYPE    18                         0    19
D37V6, multiclass
                           clus
vv                          CS MUTATED CS WILD-TYPE
  ASIAN                              0           18
  BLACK OR AFRICAN AMERICAN          1            0
  WHITE                              2           19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
              cls
clus            0  1
  CS MUTATED    1  2
  CS WILD-TYPE 11 26
[1] "tbl2"
              cls
clus           [,1] [,2]
  CS MUTATED      1    2
  CS WILD-TYPE   11   26
                        clus
vv                       CS MUTATED CS WILD-TYPE
  HISPANIC OR LATINO              1           11
  NOT HISPANIC OR LATINO          2           26
[1] 2 2
[1] FALSE

Clustering(38) Variable = IFITM3 MUTATION ANALYSIS
D38V1, survival
                  sevent
clus2               0  1
  IFITM3 MUTATED    3  1
  IFITM3 WILD-TYPE 31  5
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               4               36 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               1                5 
$`IFITM3 MUTATED`
TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-G8-6324 
       35.54        31.73        24.69        41.16 

$`IFITM3 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8047 TCGA-FF-8061 
        8.15        14.04        18.18        31.10         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       98.07        51.98        42.71        43.86        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  IFITM3 MUTATED IFITM3 WILD-TYPE 
           24.69             0.03 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
           41.16           128.12 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
          33.635           24.885 
[1] "24.7 - 41.2 (33.6)" "0.0 - 128.1 (24.9)"
[1] "hr=" "1.5"
D38V2, continuous
D38V3, binary
                  cls
clus                0  1
  IFITM3 MUTATED    3  1
  IFITM3 WILD-TYPE 21 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      3    1
  IFITM3 WILD-TYPE   21   15
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  FEMALE              3               21
  MALE                1               15
[1] 2 2
[1] FALSE
D38V4, binary
                  cls
clus                0  1
  IFITM3 MUTATED    4  0
  IFITM3 WILD-TYPE 29  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      4    0
  IFITM3 WILD-TYPE   29    6
     clus
vv    IFITM3 MUTATED IFITM3 WILD-TYPE
  NO               4               29
  YES              0                6
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  IFITM3 MUTATED                                                                                   3
  IFITM3 WILD-TYPE                                                                                30
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  IFITM3 MUTATED                          0                                  1
  IFITM3 WILD-TYPE                        3                                  3
D38V5, multiclass
                                                                                   clus
vv                                                                                  IFITM3 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              3
  PRIMARY DLBCL OF THE CNS                                                                       0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             1
                                                                                   clus
vv                                                                                  IFITM3 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               30
  PRIMARY DLBCL OF THE CNS                                                                         3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IFITM3 MUTATED       3                         1     0
  IFITM3 WILD-TYPE    15                         0    21
D38V6, multiclass
                           clus
vv                          IFITM3 MUTATED IFITM3 WILD-TYPE
  ASIAN                                  3               15
  BLACK OR AFRICAN AMERICAN              1                0
  WHITE                                  0               21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                  cls
clus                0  1
  IFITM3 MUTATED    0  4
  IFITM3 WILD-TYPE 12 24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      0    4
  IFITM3 WILD-TYPE   12   24
                        clus
vv                       IFITM3 MUTATED IFITM3 WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              4               24
[1] 2 2
[1] FALSE

Clustering(39) Variable = RANBP2 MUTATION ANALYSIS
D39V1, survival
                  sevent
clus2               0  1
  RANBP2 MUTATED    3  2
  RANBP2 WILD-TYPE 31  4
  RANBP2 MUTATED RANBP2 WILD-TYPE 
               5               35 
  RANBP2 MUTATED RANBP2 WILD-TYPE 
               2                4 
$`RANBP2 MUTATED`
TCGA-FF-8047 TCGA-FM-8000 TCGA-G8-6324 TCGA-GS-A9TV TCGA-GS-A9U4 
        4.14        31.96        41.16        24.00        12.85 

$`RANBP2 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
       24.69        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       12.66        98.07        51.98        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       32.28        38.24       128.12        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        25.91         0.03         0.56 

  RANBP2 MUTATED RANBP2 WILD-TYPE 
            4.14             0.03 
  RANBP2 MUTATED RANBP2 WILD-TYPE 
           41.16           128.12 
  RANBP2 MUTATED RANBP2 WILD-TYPE 
           24.00            25.91 
[1] "4.1 - 41.2 (24.0)"  "0.0 - 128.1 (25.9)"
[1] "hr=" "3.7"
D39V2, continuous
D39V3, binary
                  cls
clus                0  1
  RANBP2 MUTATED    5  0
  RANBP2 WILD-TYPE 19 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP2 MUTATED      5    0
  RANBP2 WILD-TYPE   19   16
        clus
vv       RANBP2 MUTATED RANBP2 WILD-TYPE
  FEMALE              5               19
  MALE                0               16
[1] 2 2
[1] FALSE
D39V4, binary
                  cls
clus                0  1
  RANBP2 MUTATED    4  1
  RANBP2 WILD-TYPE 29  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP2 MUTATED      4    1
  RANBP2 WILD-TYPE   29    5
     clus
vv    RANBP2 MUTATED RANBP2 WILD-TYPE
  NO               4               29
  YES              1                5
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  RANBP2 MUTATED                                                                                   4
  RANBP2 WILD-TYPE                                                                                29
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  RANBP2 MUTATED                          0                                  1
  RANBP2 WILD-TYPE                        3                                  3
D39V5, multiclass
                                                                                   clus
vv                                                                                  RANBP2 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              4
  PRIMARY DLBCL OF THE CNS                                                                       0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             1
                                                                                   clus
vv                                                                                  RANBP2 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               29
  PRIMARY DLBCL OF THE CNS                                                                         3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RANBP2 MUTATED       1                         1     3
  RANBP2 WILD-TYPE    17                         0    18
D39V6, multiclass
                           clus
vv                          RANBP2 MUTATED RANBP2 WILD-TYPE
  ASIAN                                  1               17
  BLACK OR AFRICAN AMERICAN              1                0
  WHITE                                  3               18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                  cls
clus                0  1
  RANBP2 MUTATED    2  3
  RANBP2 WILD-TYPE 10 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP2 MUTATED      2    3
  RANBP2 WILD-TYPE   10   25
                        clus
vv                       RANBP2 MUTATED RANBP2 WILD-TYPE
  HISPANIC OR LATINO                  2               10
  NOT HISPANIC OR LATINO              3               25
[1] 2 2
[1] FALSE

Clustering(40) Variable = KLHL6 MUTATION ANALYSIS
D40V1, survival
                 sevent
clus2              0  1
  KLHL6 MUTATED    6  0
  KLHL6 WILD-TYPE 28  6
  KLHL6 MUTATED KLHL6 WILD-TYPE 
              6              34 
  KLHL6 MUTATED KLHL6 WILD-TYPE 
              0               6 
$`KLHL6 MUTATED`
TCGA-FF-8047 TCGA-FF-8062 TCGA-FF-A7CW TCGA-FM-8000 TCGA-GR-A4D6 TCGA-GR-A4D9 
        4.14        22.32        26.01        31.96        43.86        57.17 

$`KLHL6 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CX TCGA-G8-6324 
       24.69        27.35         9.80        10.29        12.66        41.16 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU 
       98.07        51.98        42.71        32.28        38.24       128.12 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 
       24.00        53.16        45.14       109.58        25.15       111.58 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85        25.91         0.03         0.56 

  KLHL6 MUTATED KLHL6 WILD-TYPE 
           4.14            0.03 
  KLHL6 MUTATED KLHL6 WILD-TYPE 
          57.17          128.12 
  KLHL6 MUTATED KLHL6 WILD-TYPE 
         28.985          24.920 
[1] "4.1 - 57.2 (29.0)"  "0.0 - 128.1 (24.9)"
[1] "hr="     "2.4e+08"
D40V2, continuous
D40V3, binary
                 cls
clus               0  1
  KLHL6 MUTATED    5  1
  KLHL6 WILD-TYPE 19 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL6 MUTATED      5    1
  KLHL6 WILD-TYPE   19   15
        clus
vv       KLHL6 MUTATED KLHL6 WILD-TYPE
  FEMALE             5              19
  MALE               1              15
[1] 2 2
[1] FALSE
D40V4, binary
                 cls
clus               0  1
  KLHL6 MUTATED    6  0
  KLHL6 WILD-TYPE 27  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL6 MUTATED      6    0
  KLHL6 WILD-TYPE   27    6
     clus
vv    KLHL6 MUTATED KLHL6 WILD-TYPE
  NO              6              27
  YES             0               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  KLHL6 MUTATED                                                                                   6
  KLHL6 WILD-TYPE                                                                                27
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  KLHL6 MUTATED                          0                                  0
  KLHL6 WILD-TYPE                        3                                  4
D40V5, multiclass
                                                                                   clus
vv                                                                                  KLHL6 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             6
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  KLHL6 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              27
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KLHL6 MUTATED       4                         0     2
  KLHL6 WILD-TYPE    14                         1    19
D40V6, multiclass
                           clus
vv                          KLHL6 MUTATED KLHL6 WILD-TYPE
  ASIAN                                 4              14
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 2              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                 cls
clus               0  1
  KLHL6 MUTATED    0  6
  KLHL6 WILD-TYPE 12 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL6 MUTATED      0    6
  KLHL6 WILD-TYPE   12   22
                        clus
vv                       KLHL6 MUTATED KLHL6 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             6              22
[1] 2 2
[1] FALSE

Clustering(41) Variable = ZNF814 MUTATION ANALYSIS
D41V1, survival
                  sevent
clus2               0  1
  ZNF814 MUTATED    8  2
  ZNF814 WILD-TYPE 26  4
  ZNF814 MUTATED ZNF814 WILD-TYPE 
              10               30 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2                4 
$`ZNF814 MUTATED`
TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FF-8041 TCGA-FF-A7CQ TCGA-G8-6324 TCGA-GS-A9TT 
       24.62        23.64        35.54         9.80        41.16        38.24 
TCGA-GS-A9TU TCGA-GS-A9TW TCGA-GS-A9U3 TCGA-GS-A9U4 
      128.12        53.16       111.58        12.85 

$`ZNF814 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34         4.34        23.28         1.91         8.15        14.04 
TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       18.18        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-7353 
       22.32        10.29        26.01        12.66        31.96        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TV 
       51.98        42.71        43.86        57.17        32.28        24.00 
TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       45.14       109.58        25.15        25.91         0.03         0.56 

  ZNF814 MUTATED ZNF814 WILD-TYPE 
            9.80             0.03 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
          128.12           109.58 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
           36.89            24.92 
[1] "9.8 - 128.1 (36.9)" "0.0 - 109.6 (24.9)"
[1] "hr=" "1.2"
D41V2, continuous
D41V3, binary
                  cls
clus                0  1
  ZNF814 MUTATED    7  3
  ZNF814 WILD-TYPE 17 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      7    3
  ZNF814 WILD-TYPE   17   13
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  FEMALE              7               17
  MALE                3               13
[1] 2 2
[1] FALSE
D41V4, binary
                  cls
clus                0  1
  ZNF814 MUTATED    7  3
  ZNF814 WILD-TYPE 26  3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      7    3
  ZNF814 WILD-TYPE   26    3
     clus
vv    ZNF814 MUTATED ZNF814 WILD-TYPE
  NO               7               26
  YES              3                3
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  ZNF814 MUTATED                                                                                   8
  ZNF814 WILD-TYPE                                                                                25
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  ZNF814 MUTATED                          0                                  2
  ZNF814 WILD-TYPE                        3                                  2
D41V5, multiclass
                                                                                   clus
vv                                                                                  ZNF814 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              8
  PRIMARY DLBCL OF THE CNS                                                                       0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             2
                                                                                   clus
vv                                                                                  ZNF814 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               25
  PRIMARY DLBCL OF THE CNS                                                                         3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF814 MUTATED       4                         1     5
  ZNF814 WILD-TYPE    14                         0    16
D41V6, multiclass
                           clus
vv                          ZNF814 MUTATED ZNF814 WILD-TYPE
  ASIAN                                  4               14
  BLACK OR AFRICAN AMERICAN              1                0
  WHITE                                  5               16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                  cls
clus                0  1
  ZNF814 MUTATED    5  5
  ZNF814 WILD-TYPE  7 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      5    5
  ZNF814 WILD-TYPE    7   23
                        clus
vv                       ZNF814 MUTATED ZNF814 WILD-TYPE
  HISPANIC OR LATINO                  5                7
  NOT HISPANIC OR LATINO              5               23
[1] 2 2
[1] FALSE

Clustering(42) Variable = CYP4A11 MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  CYP4A11 MUTATED    2  2
  CYP4A11 WILD-TYPE 32  4
  CYP4A11 MUTATED CYP4A11 WILD-TYPE 
                4                36 
  CYP4A11 MUTATED CYP4A11 WILD-TYPE 
                2                 4 
$`CYP4A11 MUTATED`
TCGA-FA-A4XK TCGA-FF-8046 TCGA-FF-8061 TCGA-G8-6324 
       23.28        24.69        27.35        41.16 

$`CYP4A11 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         1.91        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 
       14.04        18.18        35.54        31.10        31.73         4.14 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       98.07        51.98        42.71        43.86        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  CYP4A11 MUTATED CYP4A11 WILD-TYPE 
            23.28              0.03 
  CYP4A11 MUTATED CYP4A11 WILD-TYPE 
            41.16            128.12 
  CYP4A11 MUTATED CYP4A11 WILD-TYPE 
            26.02             25.53 
[1] "23.3 - 41.2 (26.0)" "0.0 - 128.1 (25.5)"
[1] "hr=" "3.7"
D42V2, continuous
D42V3, binary
                   cls
clus                 0  1
  CYP4A11 MUTATED    1  3
  CYP4A11 WILD-TYPE 23 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A11 MUTATED      1    3
  CYP4A11 WILD-TYPE   23   13
        clus
vv       CYP4A11 MUTATED CYP4A11 WILD-TYPE
  FEMALE               1                23
  MALE                 3                13
[1] 2 2
[1] FALSE
D42V4, binary
                   cls
clus                 0  1
  CYP4A11 MUTATED    4  0
  CYP4A11 WILD-TYPE 29  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A11 MUTATED      4    0
  CYP4A11 WILD-TYPE   29    6
     clus
vv    CYP4A11 MUTATED CYP4A11 WILD-TYPE
  NO                4                29
  YES               0                 6
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  CYP4A11 MUTATED                                                                                   4
  CYP4A11 WILD-TYPE                                                                                29
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  CYP4A11 MUTATED                          0                                  0
  CYP4A11 WILD-TYPE                        3                                  4
D42V5, multiclass
                                                                                   clus
vv                                                                                  CYP4A11 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               4
  PRIMARY DLBCL OF THE CNS                                                                        0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              0
                                                                                   clus
vv                                                                                  CYP4A11 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                29
  PRIMARY DLBCL OF THE CNS                                                                          3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CYP4A11 MUTATED       3                         1     0
  CYP4A11 WILD-TYPE    15                         0    21
D42V6, multiclass
                           clus
vv                          CYP4A11 MUTATED CYP4A11 WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                   0                21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                   cls
clus                 0  1
  CYP4A11 MUTATED    0  4
  CYP4A11 WILD-TYPE 12 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A11 MUTATED      0    4
  CYP4A11 WILD-TYPE   12   24
                        clus
vv                       CYP4A11 MUTATED CYP4A11 WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               4                24
[1] 2 2
[1] FALSE

Clustering(43) Variable = PIM1 MUTATION ANALYSIS
D43V1, survival
                sevent
clus2             0  1
  PIM1 MUTATED    7  1
  PIM1 WILD-TYPE 27  5
  PIM1 MUTATED PIM1 WILD-TYPE 
             8             32 
  PIM1 MUTATED PIM1 WILD-TYPE 
             1              5 
$`PIM1 MUTATED`
TCGA-FA-A7DS TCGA-FA-A82F TCGA-FF-8061 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-GS-A9TT 
       23.64        14.04        27.35         9.80        10.29        38.24 
TCGA-RQ-A68N TCGA-RQ-AAAT 
       25.91         0.56 

$`PIM1 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7Q1 
        4.34         4.34        23.28         1.91        24.62         8.15 
TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       18.18        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8062 TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-7353 
       22.32        26.01        12.66        31.96        41.16        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TU 
       51.98        42.71        43.86        57.17        32.28       128.12 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 
       24.00        53.16        45.14       109.58        25.15       111.58 
TCGA-GS-A9U4 TCGA-RQ-A6JB 
       12.85         0.03 

  PIM1 MUTATED PIM1 WILD-TYPE 
          0.56           0.03 
  PIM1 MUTATED PIM1 WILD-TYPE 
         38.24         128.12 
  PIM1 MUTATED PIM1 WILD-TYPE 
        18.840         28.555 
[1] "0.6 - 38.2 (18.8)"  "0.0 - 128.1 (28.6)"
[1] "hr=" "1.1"
D43V2, continuous
D43V3, binary
                cls
clus              0  1
  PIM1 MUTATED    3  5
  PIM1 WILD-TYPE 21 11
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIM1 MUTATED      3    5
  PIM1 WILD-TYPE   21   11
        clus
vv       PIM1 MUTATED PIM1 WILD-TYPE
  FEMALE            3             21
  MALE              5             11
[1] 2 2
[1] FALSE
D43V4, binary
                cls
clus              0  1
  PIM1 MUTATED    7  1
  PIM1 WILD-TYPE 26  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIM1 MUTATED      7    1
  PIM1 WILD-TYPE   26    5
     clus
vv    PIM1 MUTATED PIM1 WILD-TYPE
  NO             7             26
  YES            1              5
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  PIM1 MUTATED                                                                                   6
  PIM1 WILD-TYPE                                                                                27
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  PIM1 MUTATED                          2                                  0
  PIM1 WILD-TYPE                        1                                  4
D43V5, multiclass
                                                                                   clus
vv                                                                                  PIM1 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)            6
  PRIMARY DLBCL OF THE CNS                                                                     2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                           0
                                                                                   clus
vv                                                                                  PIM1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             27
  PRIMARY DLBCL OF THE CNS                                                                       1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIM1 MUTATED       5                         0     3
  PIM1 WILD-TYPE    13                         1    18
D43V6, multiclass
                           clus
vv                          PIM1 MUTATED PIM1 WILD-TYPE
  ASIAN                                5             13
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                3             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                cls
clus              0  1
  PIM1 MUTATED    3  5
  PIM1 WILD-TYPE  9 23
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIM1 MUTATED      3    5
  PIM1 WILD-TYPE    9   23
                        clus
vv                       PIM1 MUTATED PIM1 WILD-TYPE
  HISPANIC OR LATINO                3              9
  NOT HISPANIC OR LATINO            5             23
[1] 2 2
[1] FALSE

Clustering(44) Variable = POTEE MUTATION ANALYSIS
D44V1, survival
                 sevent
clus2              0  1
  POTEE MUTATED    6  1
  POTEE WILD-TYPE 28  5
  POTEE MUTATED POTEE WILD-TYPE 
              7              33 
  POTEE MUTATED POTEE WILD-TYPE 
              1               5 
$`POTEE MUTATED`
TCGA-FA-8693 TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8061 TCGA-FM-8000 TCGA-G8-6324 
        4.34        35.54        31.10        27.35        31.96        41.16 
TCGA-GR-7353 
       98.07 

$`POTEE WILD-TYPE`
TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34        23.28         1.91        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8062 
       14.04        18.18        31.73        24.69         4.14        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-GR-A4D4 TCGA-GR-A4D5 
        9.80        10.29        26.01        12.66        51.98        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV 
       43.86        57.17        32.28        38.24       128.12        24.00 
TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 
       53.16        45.14       109.58        25.15       111.58        12.85 
TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.91         0.03         0.56 

  POTEE MUTATED POTEE WILD-TYPE 
           4.34            0.03 
  POTEE MUTATED POTEE WILD-TYPE 
          98.07          128.12 
  POTEE MUTATED POTEE WILD-TYPE 
          31.96           24.62 
[1] "4.3 - 98.1 (32.0)"  "0.0 - 128.1 (24.6)"
[1] "hr=" "1.2"
D44V2, continuous
D44V3, binary
                 cls
clus               0  1
  POTEE MUTATED    4  3
  POTEE WILD-TYPE 20 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEE MUTATED      4    3
  POTEE WILD-TYPE   20   13
        clus
vv       POTEE MUTATED POTEE WILD-TYPE
  FEMALE             4              20
  MALE               3              13
[1] 2 2
[1] FALSE
D44V4, binary
                 cls
clus               0  1
  POTEE MUTATED    7  0
  POTEE WILD-TYPE 26  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEE MUTATED      7    0
  POTEE WILD-TYPE   26    6
     clus
vv    POTEE MUTATED POTEE WILD-TYPE
  NO              7              26
  YES             0               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  POTEE MUTATED                                                                                   6
  POTEE WILD-TYPE                                                                                27
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  POTEE MUTATED                          0                                  1
  POTEE WILD-TYPE                        3                                  3
D44V5, multiclass
                                                                                   clus
vv                                                                                  POTEE MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             6
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            1
                                                                                   clus
vv                                                                                  POTEE WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              27
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  POTEE MUTATED       3                         1     3
  POTEE WILD-TYPE    15                         0    18
D44V6, multiclass
                           clus
vv                          POTEE MUTATED POTEE WILD-TYPE
  ASIAN                                 3              15
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 3              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                 cls
clus               0  1
  POTEE MUTATED    0  7
  POTEE WILD-TYPE 12 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POTEE MUTATED      0    7
  POTEE WILD-TYPE   12   21
                        clus
vv                       POTEE MUTATED POTEE WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             7              21
[1] 2 2
[1] FALSE

Clustering(45) Variable = OR52E6 MUTATION ANALYSIS
D45V1, survival
                  sevent
clus2               0  1
  OR52E6 MUTATED    1  2
  OR52E6 WILD-TYPE 33  4
  OR52E6 MUTATED OR52E6 WILD-TYPE 
               3               37 
  OR52E6 MUTATED OR52E6 WILD-TYPE 
               2                4 
$`OR52E6 MUTATED`
TCGA-FA-A4XK TCGA-G8-6324 TCGA-GR-7353 
       23.28        41.16        98.07 

$`OR52E6 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         1.91        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       12.66        31.96        51.98        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       32.28        38.24       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  OR52E6 MUTATED OR52E6 WILD-TYPE 
           23.28             0.03 
  OR52E6 MUTATED OR52E6 WILD-TYPE 
           98.07           128.12 
  OR52E6 MUTATED OR52E6 WILD-TYPE 
           41.16            25.15 
[1] "23.3 - 98.1 (41.2)" "0.0 - 128.1 (25.1)"
[1] "hr=" "4.2"
D45V2, continuous
D45V3, binary
                  cls
clus                0  1
  OR52E6 MUTATED    1  2
  OR52E6 WILD-TYPE 23 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52E6 MUTATED      1    2
  OR52E6 WILD-TYPE   23   14
        clus
vv       OR52E6 MUTATED OR52E6 WILD-TYPE
  FEMALE              1               23
  MALE                2               14
[1] 2 2
[1] FALSE
D45V4, binary
                  cls
clus                0  1
  OR52E6 MUTATED    3  0
  OR52E6 WILD-TYPE 30  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52E6 MUTATED      3    0
  OR52E6 WILD-TYPE   30    6
     clus
vv    OR52E6 MUTATED OR52E6 WILD-TYPE
  NO               3               30
  YES              0                6
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  OR52E6 MUTATED                                                                                   3
  OR52E6 WILD-TYPE                                                                                30
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  OR52E6 MUTATED                          0                                  0
  OR52E6 WILD-TYPE                        3                                  4
D45V5, multiclass
                                                                                   clus
vv                                                                                  OR52E6 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              3
  PRIMARY DLBCL OF THE CNS                                                                       0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             0
                                                                                   clus
vv                                                                                  OR52E6 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               30
  PRIMARY DLBCL OF THE CNS                                                                         3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR52E6 MUTATED       1                         1     1
  OR52E6 WILD-TYPE    17                         0    20
D45V6, multiclass
                           clus
vv                          OR52E6 MUTATED OR52E6 WILD-TYPE
  ASIAN                                  1               17
  BLACK OR AFRICAN AMERICAN              1                0
  WHITE                                  1               20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                  cls
clus                0  1
  OR52E6 MUTATED    0  3
  OR52E6 WILD-TYPE 12 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52E6 MUTATED      0    3
  OR52E6 WILD-TYPE   12   25
                        clus
vv                       OR52E6 MUTATED OR52E6 WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              3               25
[1] 2 2
[1] FALSE

Clustering(46) Variable = NBPF10 MUTATION ANALYSIS
D46V1, survival
                  sevent
clus2               0  1
  NBPF10 MUTATED    7  1
  NBPF10 WILD-TYPE 27  5
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               8               32 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
               1                5 
$`NBPF10 MUTATED`
TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FF-8047 TCGA-FF-A7CQ TCGA-FF-A7CX TCGA-GS-A9TU 
        4.34        23.28         4.14         9.80        12.66       128.12 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

$`NBPF10 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34         1.91        24.62        23.64         8.15        14.04 
TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8061 
       18.18        35.54        31.10        31.73        24.69        27.35 
TCGA-FF-8062 TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-7353 
       22.32        10.29        26.01        31.96        41.16        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT 
       51.98        42.71        43.86        57.17        32.28        38.24 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 
       24.00        53.16        45.14       109.58        25.15       111.58 
TCGA-GS-A9U4 TCGA-RQ-A68N 
       12.85        25.91 

  NBPF10 MUTATED NBPF10 WILD-TYPE 
            0.03             1.91 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
          128.12           111.58 
  NBPF10 MUTATED NBPF10 WILD-TYPE 
           7.070           29.225 
[1] "0.0 - 128.1 (7.1)"  "1.9 - 111.6 (29.2)"
[1] "hr=" "1.8"
D46V2, continuous
D46V3, binary
                  cls
clus                0  1
  NBPF10 MUTATED    3  5
  NBPF10 WILD-TYPE 21 11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      3    5
  NBPF10 WILD-TYPE   21   11
        clus
vv       NBPF10 MUTATED NBPF10 WILD-TYPE
  FEMALE              3               21
  MALE                5               11
[1] 2 2
[1] FALSE
D46V4, binary
                  cls
clus                0  1
  NBPF10 MUTATED    6  1
  NBPF10 WILD-TYPE 27  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      6    1
  NBPF10 WILD-TYPE   27    5
     clus
vv    NBPF10 MUTATED NBPF10 WILD-TYPE
  NO               6               27
  YES              1                5
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  NBPF10 MUTATED                                                                                   6
  NBPF10 WILD-TYPE                                                                                27
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  NBPF10 MUTATED                          2                                  0
  NBPF10 WILD-TYPE                        1                                  4
D46V5, multiclass
                                                                                   clus
vv                                                                                  NBPF10 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              6
  PRIMARY DLBCL OF THE CNS                                                                       2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             0
                                                                                   clus
vv                                                                                  NBPF10 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               27
  PRIMARY DLBCL OF THE CNS                                                                         1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBPF10 MUTATED       4                         0     4
  NBPF10 WILD-TYPE    14                         1    17
D46V6, multiclass
                           clus
vv                          NBPF10 MUTATED NBPF10 WILD-TYPE
  ASIAN                                  4               14
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  4               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                  cls
clus                0  1
  NBPF10 MUTATED    2  6
  NBPF10 WILD-TYPE 10 22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF10 MUTATED      2    6
  NBPF10 WILD-TYPE   10   22
                        clus
vv                       NBPF10 MUTATED NBPF10 WILD-TYPE
  HISPANIC OR LATINO                  2               10
  NOT HISPANIC OR LATINO              6               22
[1] 2 2
[1] FALSE

Clustering(47) Variable = PRB2 MUTATION ANALYSIS
D47V1, survival
                sevent
clus2             0  1
  PRB2 MUTATED    6  2
  PRB2 WILD-TYPE 28  4
  PRB2 MUTATED PRB2 WILD-TYPE 
             8             32 
  PRB2 MUTATED PRB2 WILD-TYPE 
             2              4 
$`PRB2 MUTATED`
TCGA-FA-A6HN TCGA-FF-8047 TCGA-FM-8000 TCGA-G8-6324 TCGA-GS-A9TV TCGA-GS-A9TY 
        1.91         4.14        31.96        41.16        24.00       109.58 
TCGA-GS-A9TZ TCGA-RQ-AAAT 
       25.15         0.56 

$`PRB2 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        23.28        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       98.07        51.98        42.71        43.86        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9U3 TCGA-GS-A9U4 
       38.24       128.12        53.16        45.14       111.58        12.85 
TCGA-RQ-A68N TCGA-RQ-A6JB 
       25.91         0.03 

  PRB2 MUTATED PRB2 WILD-TYPE 
          0.56           0.03 
  PRB2 MUTATED PRB2 WILD-TYPE 
        109.58         128.12 
  PRB2 MUTATED PRB2 WILD-TYPE 
        24.575         25.960 
[1] "0.6 - 109.6 (24.6)" "0.0 - 128.1 (26.0)"
[1] "hr=" "2.4"
D47V2, continuous
D47V3, binary
                cls
clus              0  1
  PRB2 MUTATED    6  2
  PRB2 WILD-TYPE 18 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      6    2
  PRB2 WILD-TYPE   18   14
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  FEMALE            6             18
  MALE              2             14
[1] 2 2
[1] FALSE
D47V4, binary
                cls
clus              0  1
  PRB2 MUTATED    6  2
  PRB2 WILD-TYPE 27  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      6    2
  PRB2 WILD-TYPE   27    4
     clus
vv    PRB2 MUTATED PRB2 WILD-TYPE
  NO             6             27
  YES            2              4
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  PRB2 MUTATED                                                                                   5
  PRB2 WILD-TYPE                                                                                28
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  PRB2 MUTATED                          1                                  2
  PRB2 WILD-TYPE                        2                                  2
D47V5, multiclass
                                                                                   clus
vv                                                                                  PRB2 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)            5
  PRIMARY DLBCL OF THE CNS                                                                     1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                           2
                                                                                   clus
vv                                                                                  PRB2 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             28
  PRIMARY DLBCL OF THE CNS                                                                       2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRB2 MUTATED       2                         1     5
  PRB2 WILD-TYPE    16                         0    16
D47V6, multiclass
                           clus
vv                          PRB2 MUTATED PRB2 WILD-TYPE
  ASIAN                                2             16
  BLACK OR AFRICAN AMERICAN            1              0
  WHITE                                5             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                cls
clus              0  1
  PRB2 MUTATED    4  4
  PRB2 WILD-TYPE  8 24
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      4    4
  PRB2 WILD-TYPE    8   24
                        clus
vv                       PRB2 MUTATED PRB2 WILD-TYPE
  HISPANIC OR LATINO                4              8
  NOT HISPANIC OR LATINO            4             24
[1] 2 2
[1] FALSE

Clustering(48) Variable = MUC6 MUTATION ANALYSIS
D48V1, survival
                sevent
clus2             0  1
  MUC6 MUTATED   18  3
  MUC6 WILD-TYPE 16  3
  MUC6 MUTATED MUC6 WILD-TYPE 
            21             19 
  MUC6 MUTATED MUC6 WILD-TYPE 
             3              3 
$`MUC6 MUTATED`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8046 
        4.34         4.34         8.15        14.04        18.18        24.69 
TCGA-FF-8047 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-7353 
        4.14         9.80        10.29        31.96        41.16        98.07 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TW 
       42.71        43.86        57.17        38.24       128.12        53.16 
TCGA-GS-A9U3 TCGA-RQ-A68N TCGA-RQ-A6JB 
      111.58        25.91         0.03 

$`MUC6 WILD-TYPE`
TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FF-8041 TCGA-FF-8042 
       23.28         1.91        24.62        23.64        35.54        31.10 
TCGA-FF-8043 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CW TCGA-FF-A7CX TCGA-GR-A4D4 
       31.73        27.35        22.32        26.01        12.66        51.98 
TCGA-GS-A9TQ TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U4 
       32.28        24.00        45.14       109.58        25.15        12.85 
TCGA-RQ-AAAT 
        0.56 

  MUC6 MUTATED MUC6 WILD-TYPE 
          0.03           0.56 
  MUC6 MUTATED MUC6 WILD-TYPE 
        128.12         109.58 
  MUC6 MUTATED MUC6 WILD-TYPE 
         25.91          25.15 
[1] "0.0 - 128.1 (25.9)" "0.6 - 109.6 (25.1)"
[1] "hr=" "1.1"
D48V2, continuous
D48V3, binary
                cls
clus              0  1
  MUC6 MUTATED   12  9
  MUC6 WILD-TYPE 12  7
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED     12    9
  MUC6 WILD-TYPE   12    7
        clus
vv       MUC6 MUTATED MUC6 WILD-TYPE
  FEMALE           12             12
  MALE              9              7
[1] 2 2
[1] FALSE
D48V4, binary
                cls
clus              0  1
  MUC6 MUTATED   17  3
  MUC6 WILD-TYPE 16  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED     17    3
  MUC6 WILD-TYPE   16    3
     clus
vv    MUC6 MUTATED MUC6 WILD-TYPE
  NO            17             16
  YES            3              3
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  MUC6 MUTATED                                                                                  18
  MUC6 WILD-TYPE                                                                                15
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  MUC6 MUTATED                          2                                  1
  MUC6 WILD-TYPE                        1                                  3
D48V5, multiclass
                                                                                   clus
vv                                                                                  MUC6 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)           18
  PRIMARY DLBCL OF THE CNS                                                                     2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                           1
                                                                                   clus
vv                                                                                  MUC6 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             15
  PRIMARY DLBCL OF THE CNS                                                                       1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MUC6 MUTATED       7                         1    13
  MUC6 WILD-TYPE    11                         0     8
D48V6, multiclass
                           clus
vv                          MUC6 MUTATED MUC6 WILD-TYPE
  ASIAN                                7             11
  BLACK OR AFRICAN AMERICAN            1              0
  WHITE                               13              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                cls
clus              0  1
  MUC6 MUTATED    5 16
  MUC6 WILD-TYPE  7 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC6 MUTATED      5   16
  MUC6 WILD-TYPE    7   12
                        clus
vv                       MUC6 MUTATED MUC6 WILD-TYPE
  HISPANIC OR LATINO                5              7
  NOT HISPANIC OR LATINO           16             12
[1] 2 2
[1] FALSE

Clustering(49) Variable = SALL1 MUTATION ANALYSIS
D49V1, survival
                 sevent
clus2              0  1
  SALL1 MUTATED    3  2
  SALL1 WILD-TYPE 31  4
  SALL1 MUTATED SALL1 WILD-TYPE 
              5              35 
  SALL1 MUTATED SALL1 WILD-TYPE 
              2               4 
$`SALL1 MUTATED`
TCGA-FA-A7Q1 TCGA-FF-A7CX TCGA-G8-6324 TCGA-GR-A4D4 TCGA-GS-A9TZ 
        8.15        12.66        41.16        51.98        25.15 

$`SALL1 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FM-8000 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       31.96        98.07        42.71        43.86        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
      111.58        12.85        25.91         0.03         0.56 

  SALL1 MUTATED SALL1 WILD-TYPE 
           8.15            0.03 
  SALL1 MUTATED SALL1 WILD-TYPE 
          51.98          128.12 
  SALL1 MUTATED SALL1 WILD-TYPE 
          25.15           25.91 
[1] "8.2 - 52.0 (25.1)"  "0.0 - 128.1 (25.9)"
[1] "hr=" "3.3"
D49V2, continuous
D49V3, binary
                 cls
clus               0  1
  SALL1 MUTATED    3  2
  SALL1 WILD-TYPE 21 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL1 MUTATED      3    2
  SALL1 WILD-TYPE   21   14
        clus
vv       SALL1 MUTATED SALL1 WILD-TYPE
  FEMALE             3              21
  MALE               2              14
[1] 2 2
[1] FALSE
D49V4, binary
                 cls
clus               0  1
  SALL1 MUTATED    4  1
  SALL1 WILD-TYPE 29  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL1 MUTATED      4    1
  SALL1 WILD-TYPE   29    5
     clus
vv    SALL1 MUTATED SALL1 WILD-TYPE
  NO              4              29
  YES             1               5
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  SALL1 MUTATED                                                                                   4
  SALL1 WILD-TYPE                                                                                29
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  SALL1 MUTATED                          0                                  1
  SALL1 WILD-TYPE                        3                                  3
D49V5, multiclass
                                                                                   clus
vv                                                                                  SALL1 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             4
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            1
                                                                                   clus
vv                                                                                  SALL1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              29
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SALL1 MUTATED       2                         1     2
  SALL1 WILD-TYPE    16                         0    19
D49V6, multiclass
                           clus
vv                          SALL1 MUTATED SALL1 WILD-TYPE
  ASIAN                                 2              16
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 2              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                 cls
clus               0  1
  SALL1 MUTATED    1  4
  SALL1 WILD-TYPE 11 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SALL1 MUTATED      1    4
  SALL1 WILD-TYPE   11   24
                        clus
vv                       SALL1 MUTATED SALL1 WILD-TYPE
  HISPANIC OR LATINO                 1              11
  NOT HISPANIC OR LATINO             4              24
[1] 2 2
[1] FALSE

Clustering(50) Variable = PAK2 MUTATION ANALYSIS
D50V1, survival
                sevent
clus2             0  1
  PAK2 MUTATED    6  1
  PAK2 WILD-TYPE 28  5
  PAK2 MUTATED PAK2 WILD-TYPE 
             7             33 
  PAK2 MUTATED PAK2 WILD-TYPE 
             1              5 
$`PAK2 MUTATED`
TCGA-FF-8041 TCGA-FF-8047 TCGA-G8-6324 TCGA-GR-A4D9 TCGA-GS-A9TW TCGA-GS-A9U3 
       35.54         4.14        41.16        57.17        53.16       111.58 
TCGA-RQ-A6JB 
        0.03 

$`PAK2 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
        8.15        14.04        18.18        31.10        31.73        24.69 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GS-A9TQ 
       31.96        98.07        51.98        42.71        43.86        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
       38.24       128.12        24.00        45.14       109.58        25.15 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-AAAT 
       12.85        25.91         0.56 

  PAK2 MUTATED PAK2 WILD-TYPE 
          0.03           0.56 
  PAK2 MUTATED PAK2 WILD-TYPE 
        111.58         128.12 
  PAK2 MUTATED PAK2 WILD-TYPE 
         41.16          24.69 
[1] "0.0 - 111.6 (41.2)" "0.6 - 128.1 (24.7)"
[1] "hr=" "1.2"
D50V2, continuous
D50V3, binary
                cls
clus              0  1
  PAK2 MUTATED    7  0
  PAK2 WILD-TYPE 17 16
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK2 MUTATED      7    0
  PAK2 WILD-TYPE   17   16
        clus
vv       PAK2 MUTATED PAK2 WILD-TYPE
  FEMALE            7             17
  MALE              0             16
[1] 2 2
[1] FALSE
D50V4, binary
                cls
clus              0  1
  PAK2 MUTATED    5  1
  PAK2 WILD-TYPE 28  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK2 MUTATED      5    1
  PAK2 WILD-TYPE   28    5
     clus
vv    PAK2 MUTATED PAK2 WILD-TYPE
  NO             5             28
  YES            1              5
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  PAK2 MUTATED                                                                                   4
  PAK2 WILD-TYPE                                                                                29
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  PAK2 MUTATED                          1                                  2
  PAK2 WILD-TYPE                        2                                  2
D50V5, multiclass
                                                                                   clus
vv                                                                                  PAK2 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)            4
  PRIMARY DLBCL OF THE CNS                                                                     1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                           2
                                                                                   clus
vv                                                                                  PAK2 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             29
  PRIMARY DLBCL OF THE CNS                                                                       2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PAK2 MUTATED       2                         1     4
  PAK2 WILD-TYPE    16                         0    17
D50V6, multiclass
                           clus
vv                          PAK2 MUTATED PAK2 WILD-TYPE
  ASIAN                                2             16
  BLACK OR AFRICAN AMERICAN            1              0
  WHITE                                4             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                cls
clus              0  1
  PAK2 MUTATED    2  5
  PAK2 WILD-TYPE 10 23
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK2 MUTATED      2    5
  PAK2 WILD-TYPE   10   23
                        clus
vv                       PAK2 MUTATED PAK2 WILD-TYPE
  HISPANIC OR LATINO                2             10
  NOT HISPANIC OR LATINO            5             23
[1] 2 2
[1] FALSE

Clustering(51) Variable = FLG MUTATION ANALYSIS
D51V1, survival
               sevent
clus2            0  1
  FLG MUTATED   14  3
  FLG WILD-TYPE 20  3
  FLG MUTATED FLG WILD-TYPE 
           17            23 
  FLG MUTATED FLG WILD-TYPE 
            3             3 
$`FLG MUTATED`
TCGA-FA-8693 TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8042 
        4.34         1.91        23.64         8.15        14.04        31.10 
TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CX TCGA-G8-6324 
       31.73         4.14        27.35        22.32        12.66        41.16 
TCGA-GR-7353 TCGA-GS-A9TQ TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9U3 
       98.07        32.28       128.12        24.00       111.58 

$`FLG WILD-TYPE`
TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8046 
        4.34        23.28        24.62        18.18        35.54        24.69 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D5 
        9.80        10.29        26.01        31.96        51.98        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       43.86        57.17        38.24        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15        12.85        25.91         0.03         0.56 

  FLG MUTATED FLG WILD-TYPE 
         1.91          0.03 
  FLG MUTATED FLG WILD-TYPE 
       128.12        109.58 
  FLG MUTATED FLG WILD-TYPE 
        24.00         25.91 
[1] "1.9 - 128.1 (24.0)" "0.0 - 109.6 (25.9)"
[1] "hr=" "1.5"
D51V2, continuous
D51V3, binary
               cls
clus             0  1
  FLG MUTATED   11  6
  FLG WILD-TYPE 13 10
[1] "tbl2"
               cls
clus            [,1] [,2]
  FLG MUTATED     11    6
  FLG WILD-TYPE   13   10
        clus
vv       FLG MUTATED FLG WILD-TYPE
  FEMALE          11            13
  MALE             6            10
[1] 2 2
[1] FALSE
D51V4, binary
               cls
clus             0  1
  FLG MUTATED   15  2
  FLG WILD-TYPE 18  4
[1] "tbl2"
               cls
clus            [,1] [,2]
  FLG MUTATED     15    2
  FLG WILD-TYPE   18    4
     clus
vv    FLG MUTATED FLG WILD-TYPE
  NO           15            18
  YES           2             4
[1] 2 2
[1] FALSE
               vv
clus            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  FLG MUTATED                                                                                  16
  FLG WILD-TYPE                                                                                17
               vv
clus            PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  FLG MUTATED                          0                                  1
  FLG WILD-TYPE                        3                                  3
D51V5, multiclass
                                                                                   clus
vv                                                                                  FLG MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)          16
  PRIMARY DLBCL OF THE CNS                                                                    0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                          1
                                                                                   clus
vv                                                                                  FLG WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)            17
  PRIMARY DLBCL OF THE CNS                                                                      3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FLG MUTATED      10                         1     6
  FLG WILD-TYPE     8                         0    15
D51V6, multiclass
                           clus
vv                          FLG MUTATED FLG WILD-TYPE
  ASIAN                              10             8
  BLACK OR AFRICAN AMERICAN           1             0
  WHITE                               6            15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
               cls
clus             0  1
  FLG MUTATED    4 13
  FLG WILD-TYPE  8 15
[1] "tbl2"
               cls
clus            [,1] [,2]
  FLG MUTATED      4   13
  FLG WILD-TYPE    8   15
                        clus
vv                       FLG MUTATED FLG WILD-TYPE
  HISPANIC OR LATINO               4             8
  NOT HISPANIC OR LATINO          13            15
[1] 2 2
[1] FALSE

Clustering(52) Variable = MUC17 MUTATION ANALYSIS
D52V1, survival
                 sevent
clus2              0  1
  MUC17 MUTATED    9  3
  MUC17 WILD-TYPE 25  3
  MUC17 MUTATED MUC17 WILD-TYPE 
             12              28 
  MUC17 MUTATED MUC17 WILD-TYPE 
              3               3 
$`MUC17 MUTATED`
TCGA-FA-A4XK TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-A7CR TCGA-FF-A7CX 
       23.28        31.10        24.69         4.14        10.29        12.66 
TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GS-A9TQ TCGA-GS-A9TY TCGA-RQ-A68N 
       41.16        98.07        42.71        32.28       109.58        25.91 

$`MUC17 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         1.91        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8061 TCGA-FF-8062 
       14.04        18.18        35.54        31.73        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CW TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 
        9.80        26.01        31.96        51.98        43.86        57.17 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TZ 
       38.24       128.12        24.00        53.16        45.14        25.15 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB TCGA-RQ-AAAT 
      111.58        12.85         0.03         0.56 

  MUC17 MUTATED MUC17 WILD-TYPE 
           4.14            0.03 
  MUC17 MUTATED MUC17 WILD-TYPE 
         109.58          128.12 
  MUC17 MUTATED MUC17 WILD-TYPE 
         28.505          24.885 
[1] "4.1 - 109.6 (28.5)" "0.0 - 128.1 (24.9)"
[1] "hr=" "2"  
D52V2, continuous
D52V3, binary
                 cls
clus               0  1
  MUC17 MUTATED    6  6
  MUC17 WILD-TYPE 18 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED      6    6
  MUC17 WILD-TYPE   18   10
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  FEMALE             6              18
  MALE               6              10
[1] 2 2
[1] FALSE
D52V4, binary
                 cls
clus               0  1
  MUC17 MUTATED   12  0
  MUC17 WILD-TYPE 21  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED     12    0
  MUC17 WILD-TYPE   21    6
     clus
vv    MUC17 MUTATED MUC17 WILD-TYPE
  NO             12              21
  YES             0               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  MUC17 MUTATED                                                                                  11
  MUC17 WILD-TYPE                                                                                22
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  MUC17 MUTATED                          1                                  0
  MUC17 WILD-TYPE                        2                                  4
D52V5, multiclass
                                                                                   clus
vv                                                                                  MUC17 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)            11
  PRIMARY DLBCL OF THE CNS                                                                      1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  MUC17 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              22
  PRIMARY DLBCL OF THE CNS                                                                        2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MUC17 MUTATED       6                         1     5
  MUC17 WILD-TYPE    12                         0    16
D52V6, multiclass
                           clus
vv                          MUC17 MUTATED MUC17 WILD-TYPE
  ASIAN                                 6              12
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 5              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                 cls
clus               0  1
  MUC17 MUTATED    3  9
  MUC17 WILD-TYPE  9 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED      3    9
  MUC17 WILD-TYPE    9   19
                        clus
vv                       MUC17 MUTATED MUC17 WILD-TYPE
  HISPANIC OR LATINO                 3               9
  NOT HISPANIC OR LATINO             9              19
[1] 2 2
[1] FALSE

Clustering(53) Variable = OR2T4 MUTATION ANALYSIS
D53V1, survival
                 sevent
clus2              0  1
  OR2T4 MUTATED    6  2
  OR2T4 WILD-TYPE 28  4
  OR2T4 MUTATED OR2T4 WILD-TYPE 
              8              32 
  OR2T4 MUTATED OR2T4 WILD-TYPE 
              2               4 
$`OR2T4 MUTATED`
TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A82F TCGA-FF-A7CX TCGA-G8-6324 TCGA-GR-A4D5 
        4.34         1.91        14.04        12.66        41.16        42.71 
TCGA-GS-A9TV TCGA-GS-A9U3 
       24.00       111.58 

$`OR2T4 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A86F 
        4.34        23.28        24.62        23.64         8.15        18.18 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       35.54        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FM-8000 TCGA-GR-7353 
       22.32         9.80        10.29        26.01        31.96        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU 
       51.98        43.86        57.17        32.28        38.24       128.12 
TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U4 TCGA-RQ-A68N 
       53.16        45.14       109.58        25.15        12.85        25.91 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  OR2T4 MUTATED OR2T4 WILD-TYPE 
           1.91            0.03 
  OR2T4 MUTATED OR2T4 WILD-TYPE 
         111.58          128.12 
  OR2T4 MUTATED OR2T4 WILD-TYPE 
          19.02           25.96 
[1] "1.9 - 111.6 (19.0)" "0.0 - 128.1 (26.0)"
[1] "hr=" "2.1"
D53V2, continuous
D53V3, binary
                 cls
clus               0  1
  OR2T4 MUTATED    5  3
  OR2T4 WILD-TYPE 19 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T4 MUTATED      5    3
  OR2T4 WILD-TYPE   19   13
        clus
vv       OR2T4 MUTATED OR2T4 WILD-TYPE
  FEMALE             5              19
  MALE               3              13
[1] 2 2
[1] FALSE
D53V4, binary
                 cls
clus               0  1
  OR2T4 MUTATED    7  1
  OR2T4 WILD-TYPE 26  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T4 MUTATED      7    1
  OR2T4 WILD-TYPE   26    5
     clus
vv    OR2T4 MUTATED OR2T4 WILD-TYPE
  NO              7              26
  YES             1               5
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  OR2T4 MUTATED                                                                                   7
  OR2T4 WILD-TYPE                                                                                26
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  OR2T4 MUTATED                          0                                  1
  OR2T4 WILD-TYPE                        3                                  3
D53V5, multiclass
                                                                                   clus
vv                                                                                  OR2T4 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             7
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            1
                                                                                   clus
vv                                                                                  OR2T4 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              26
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR2T4 MUTATED       3                         1     4
  OR2T4 WILD-TYPE    15                         0    17
D53V6, multiclass
                           clus
vv                          OR2T4 MUTATED OR2T4 WILD-TYPE
  ASIAN                                 3              15
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 4              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                 cls
clus               0  1
  OR2T4 MUTATED    2  6
  OR2T4 WILD-TYPE 10 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2T4 MUTATED      2    6
  OR2T4 WILD-TYPE   10   22
                        clus
vv                       OR2T4 MUTATED OR2T4 WILD-TYPE
  HISPANIC OR LATINO                 2              10
  NOT HISPANIC OR LATINO             6              22
[1] 2 2
[1] FALSE

Clustering(54) Variable = AMAC1L3 MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                0  1
  AMAC1L3 MUTATED    4  1
  AMAC1L3 WILD-TYPE 30  5
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                5                35 
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                1                 5 
$`AMAC1L3 MUTATED`
TCGA-FA-8693 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-G8-6324 
        4.34        31.10        31.73        24.69        41.16 

$`AMAC1L3 WILD-TYPE`
TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34        23.28         1.91        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       14.04        18.18        35.54         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-7353 
        9.80        10.29        26.01        12.66        31.96        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT 
       51.98        42.71        43.86        57.17        32.28        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
      128.12        24.00        53.16        45.14       109.58        25.15 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
      111.58        12.85        25.91         0.03         0.56 

  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
             4.34              0.03 
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
            41.16            128.12 
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
            31.10             25.15 
[1] "4.3 - 41.2 (31.1)"  "0.0 - 128.1 (25.1)"
[1] "hr=" "1.4"
D54V2, continuous
D54V3, binary
                   cls
clus                 0  1
  AMAC1L3 MUTATED    3  2
  AMAC1L3 WILD-TYPE 21 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMAC1L3 MUTATED      3    2
  AMAC1L3 WILD-TYPE   21   14
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  FEMALE               3                21
  MALE                 2                14
[1] 2 2
[1] FALSE
D54V4, binary
                   cls
clus                 0  1
  AMAC1L3 MUTATED    5  0
  AMAC1L3 WILD-TYPE 28  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMAC1L3 MUTATED      5    0
  AMAC1L3 WILD-TYPE   28    6
     clus
vv    AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  NO                5                28
  YES               0                 6
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  AMAC1L3 MUTATED                                                                                   5
  AMAC1L3 WILD-TYPE                                                                                28
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  AMAC1L3 MUTATED                          0                                  0
  AMAC1L3 WILD-TYPE                        3                                  4
D54V5, multiclass
                                                                                   clus
vv                                                                                  AMAC1L3 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               5
  PRIMARY DLBCL OF THE CNS                                                                        0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              0
                                                                                   clus
vv                                                                                  AMAC1L3 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                28
  PRIMARY DLBCL OF THE CNS                                                                          3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMAC1L3 MUTATED       3                         1     1
  AMAC1L3 WILD-TYPE    15                         0    20
D54V6, multiclass
                           clus
vv                          AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                   1                20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                   cls
clus                 0  1
  AMAC1L3 MUTATED    0  5
  AMAC1L3 WILD-TYPE 12 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMAC1L3 MUTATED      0    5
  AMAC1L3 WILD-TYPE   12   23
                        clus
vv                       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               5                23
[1] 2 2
[1] FALSE

Clustering(55) Variable = APOB MUTATION ANALYSIS
D55V1, survival
                sevent
clus2             0  1
  APOB MUTATED    2  1
  APOB WILD-TYPE 32  5
  APOB MUTATED APOB WILD-TYPE 
             3             37 
  APOB MUTATED APOB WILD-TYPE 
             1              5 
$`APOB MUTATED`
TCGA-G8-6324 TCGA-GR-7353 TCGA-GS-A9TW 
       41.16        98.07        53.16 

$`APOB WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       24.69         4.14        27.35        22.32         9.80        10.29 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
       26.01        12.66        31.96        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TX 
       57.17        32.28        38.24       128.12        24.00        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  APOB MUTATED APOB WILD-TYPE 
         41.16           0.03 
  APOB MUTATED APOB WILD-TYPE 
         98.07         128.12 
  APOB MUTATED APOB WILD-TYPE 
         53.16          24.69 
[1] "41.2 - 98.1 (53.2)" "0.0 - 128.1 (24.7)"
[1] "hr=" "1.4"
D55V2, continuous
D55V3, binary
                cls
clus              0  1
  APOB MUTATED    2  1
  APOB WILD-TYPE 22 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED      2    1
  APOB WILD-TYPE   22   15
        clus
vv       APOB MUTATED APOB WILD-TYPE
  FEMALE            2             22
  MALE              1             15
[1] 2 2
[1] FALSE
D55V4, binary
                cls
clus              0  1
  APOB MUTATED    2  1
  APOB WILD-TYPE 31  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED      2    1
  APOB WILD-TYPE   31    5
     clus
vv    APOB MUTATED APOB WILD-TYPE
  NO             2             31
  YES            1              5
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  APOB MUTATED                                                                                   2
  APOB WILD-TYPE                                                                                31
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  APOB MUTATED                          0                                  1
  APOB WILD-TYPE                        3                                  3
D55V5, multiclass
                                                                                   clus
vv                                                                                  APOB MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)            2
  PRIMARY DLBCL OF THE CNS                                                                     0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                           1
                                                                                   clus
vv                                                                                  APOB WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             31
  PRIMARY DLBCL OF THE CNS                                                                       3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  APOB MUTATED       0                         1     2
  APOB WILD-TYPE    18                         0    19
D55V6, multiclass
                           clus
vv                          APOB MUTATED APOB WILD-TYPE
  ASIAN                                0             18
  BLACK OR AFRICAN AMERICAN            1              0
  WHITE                                2             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                cls
clus              0  1
  APOB MUTATED    1  2
  APOB WILD-TYPE 11 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED      1    2
  APOB WILD-TYPE   11   26
                        clus
vv                       APOB MUTATED APOB WILD-TYPE
  HISPANIC OR LATINO                1             11
  NOT HISPANIC OR LATINO            2             26
[1] 2 2
[1] FALSE

Clustering(56) Variable = KRTAP4-7 MUTATION ANALYSIS
D56V1, survival
                    sevent
clus2                 0  1
  KRTAP4-7 MUTATED    6  2
  KRTAP4-7 WILD-TYPE 28  4
  KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE 
                 8                 32 
  KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE 
                 2                  4 
$`KRTAP4-7 MUTATED`
TCGA-FF-8041 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8062 TCGA-FF-A7CR TCGA-FF-A7CX 
       35.54        24.69         4.14        22.32        10.29        12.66 
TCGA-G8-6324 TCGA-GS-A9TV 
       41.16        24.00 

$`KRTAP4-7 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8061 
        8.15        14.04        18.18        31.10        31.73        27.35 
TCGA-FF-A7CQ TCGA-FF-A7CW TCGA-FM-8000 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
        9.80        26.01        31.96        98.07        51.98        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TW 
       43.86        57.17        32.28        38.24       128.12        53.16 
TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N 
       45.14       109.58        25.15       111.58        12.85        25.91 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE 
              4.14               0.03 
  KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE 
             41.16             128.12 
  KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE 
             23.16              26.68 
[1] "4.1 - 41.2 (23.2)"  "0.0 - 128.1 (26.7)"
[1] "hr=" "2.4"
D56V2, continuous
D56V3, binary
                    cls
clus                  0  1
  KRTAP4-7 MUTATED    5  3
  KRTAP4-7 WILD-TYPE 19 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-7 MUTATED      5    3
  KRTAP4-7 WILD-TYPE   19   13
        clus
vv       KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE
  FEMALE                5                 19
  MALE                  3                 13
[1] 2 2
[1] FALSE
D56V4, binary
                    cls
clus                  0  1
  KRTAP4-7 MUTATED    7  1
  KRTAP4-7 WILD-TYPE 26  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-7 MUTATED      7    1
  KRTAP4-7 WILD-TYPE   26    5
     clus
vv    KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE
  NO                 7                 26
  YES                1                  5
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  KRTAP4-7 MUTATED                                                                                   6
  KRTAP4-7 WILD-TYPE                                                                                27
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  KRTAP4-7 MUTATED                          0
  KRTAP4-7 WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  KRTAP4-7 MUTATED                                    2
  KRTAP4-7 WILD-TYPE                                  2
D56V5, multiclass
                                                                                   clus
vv                                                                                  KRTAP4-7 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                6
  PRIMARY DLBCL OF THE CNS                                                                         0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               2
                                                                                   clus
vv                                                                                  KRTAP4-7 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 27
  PRIMARY DLBCL OF THE CNS                                                                           3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRTAP4-7 MUTATED       6                         1     1
  KRTAP4-7 WILD-TYPE    12                         0    20
D56V6, multiclass
                           clus
vv                          KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE
  ASIAN                                    6                 12
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                    1                 20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                    cls
clus                  0  1
  KRTAP4-7 MUTATED    1  7
  KRTAP4-7 WILD-TYPE 11 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP4-7 MUTATED      1    7
  KRTAP4-7 WILD-TYPE   11   21
                        clus
vv                       KRTAP4-7 MUTATED KRTAP4-7 WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO                7                 21
[1] 2 2
[1] FALSE

Clustering(57) Variable = MUC16 MUTATION ANALYSIS
D57V1, survival
                 sevent
clus2              0  1
  MUC16 MUTATED    8  4
  MUC16 WILD-TYPE 26  2
  MUC16 MUTATED MUC16 WILD-TYPE 
             12              28 
  MUC16 MUTATED MUC16 WILD-TYPE 
              4               2 
$`MUC16 MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8061 
       23.28         1.91        23.64        35.54        31.73        27.35 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D9 TCGA-GS-A9TV 
        9.80        10.29        41.16        98.07        57.17        24.00 

$`MUC16 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F 
        4.34         4.34        24.62         8.15        14.04        18.18 
TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8062 TCGA-FF-A7CW TCGA-FF-A7CX 
       31.10        24.69         4.14        22.32        26.01        12.66 
TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GS-A9TQ TCGA-GS-A9TT 
       31.96        51.98        42.71        43.86        32.28        38.24 
TCGA-GS-A9TU TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 
      128.12        53.16        45.14       109.58        25.15       111.58 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85        25.91         0.03         0.56 

  MUC16 MUTATED MUC16 WILD-TYPE 
           1.91            0.03 
  MUC16 MUTATED MUC16 WILD-TYPE 
          98.07          128.12 
  MUC16 MUTATED MUC16 WILD-TYPE 
         25.675          25.530 
[1] "1.9 - 98.1 (25.7)"  "0.0 - 128.1 (25.5)"
[1] "hr=" "4.4"
D57V2, continuous
D57V3, binary
                 cls
clus               0  1
  MUC16 MUTATED    6  6
  MUC16 WILD-TYPE 18 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC16 MUTATED      6    6
  MUC16 WILD-TYPE   18   10
        clus
vv       MUC16 MUTATED MUC16 WILD-TYPE
  FEMALE             6              18
  MALE               6              10
[1] 2 2
[1] FALSE
D57V4, binary
                 cls
clus               0  1
  MUC16 MUTATED   11  1
  MUC16 WILD-TYPE 22  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC16 MUTATED     11    1
  MUC16 WILD-TYPE   22    5
     clus
vv    MUC16 MUTATED MUC16 WILD-TYPE
  NO             11              22
  YES             1               5
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  MUC16 MUTATED                                                                                  10
  MUC16 WILD-TYPE                                                                                23
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  MUC16 MUTATED                          0                                  2
  MUC16 WILD-TYPE                        3                                  2
D57V5, multiclass
                                                                                   clus
vv                                                                                  MUC16 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)            10
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            2
                                                                                   clus
vv                                                                                  MUC16 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              23
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MUC16 MUTATED       8                         1     3
  MUC16 WILD-TYPE    10                         0    18
D57V6, multiclass
                           clus
vv                          MUC16 MUTATED MUC16 WILD-TYPE
  ASIAN                                 8              10
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 3              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                 cls
clus               0  1
  MUC16 MUTATED    1 11
  MUC16 WILD-TYPE 11 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC16 MUTATED      1   11
  MUC16 WILD-TYPE   11   17
                        clus
vv                       MUC16 MUTATED MUC16 WILD-TYPE
  HISPANIC OR LATINO                 1              11
  NOT HISPANIC OR LATINO            11              17
[1] 2 2
[1] FALSE

Clustering(58) Variable = NEFH MUTATION ANALYSIS
D58V1, survival
                sevent
clus2             0  1
  NEFH MUTATED    6  0
  NEFH WILD-TYPE 28  6
  NEFH MUTATED NEFH WILD-TYPE 
             6             34 
  NEFH MUTATED NEFH WILD-TYPE 
             0              6 
$`NEFH MUTATED`
TCGA-FA-8693 TCGA-FA-A7DS TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-A7CX TCGA-GR-A4D5 
        4.34        23.64        14.04        35.54        12.66        42.71 

$`NEFH WILD-TYPE`
TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FA-A86F 
        4.34        23.28         1.91        24.62         8.15        18.18 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       31.10        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-7353 
        9.80        10.29        26.01        31.96        41.16        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU 
       51.98        43.86        57.17        32.28        38.24       128.12 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 
       24.00        53.16        45.14       109.58        25.15       111.58 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85        25.91         0.03         0.56 

  NEFH MUTATED NEFH WILD-TYPE 
          4.34           0.03 
  NEFH MUTATED NEFH WILD-TYPE 
         42.71         128.12 
  NEFH MUTATED NEFH WILD-TYPE 
         18.84          25.96 
[1] "4.3 - 42.7 (18.8)"  "0.0 - 128.1 (26.0)"
[1] "hr="     "2.3e+08"
D58V2, continuous
D58V3, binary
                cls
clus              0  1
  NEFH MUTATED    4  2
  NEFH WILD-TYPE 20 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      4    2
  NEFH WILD-TYPE   20   14
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  FEMALE            4             20
  MALE              2             14
[1] 2 2
[1] FALSE
D58V4, binary
                cls
clus              0  1
  NEFH MUTATED    6  0
  NEFH WILD-TYPE 27  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      6    0
  NEFH WILD-TYPE   27    6
     clus
vv    NEFH MUTATED NEFH WILD-TYPE
  NO             6             27
  YES            0              6
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  NEFH MUTATED                                                                                   5
  NEFH WILD-TYPE                                                                                28
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  NEFH MUTATED                          0                                  1
  NEFH WILD-TYPE                        3                                  3
D58V5, multiclass
                                                                                   clus
vv                                                                                  NEFH MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)            5
  PRIMARY DLBCL OF THE CNS                                                                     0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                           1
                                                                                   clus
vv                                                                                  NEFH WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             28
  PRIMARY DLBCL OF THE CNS                                                                       3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NEFH MUTATED       4                         0     2
  NEFH WILD-TYPE    14                         1    19
D58V6, multiclass
                           clus
vv                          NEFH MUTATED NEFH WILD-TYPE
  ASIAN                                4             14
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                2             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                cls
clus              0  1
  NEFH MUTATED    0  6
  NEFH WILD-TYPE 12 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      0    6
  NEFH WILD-TYPE   12   22
                        clus
vv                       NEFH MUTATED NEFH WILD-TYPE
  HISPANIC OR LATINO                0             12
  NOT HISPANIC OR LATINO            6             22
[1] 2 2
[1] FALSE

Clustering(59) Variable = KCNN3 MUTATION ANALYSIS
D59V1, survival
                 sevent
clus2              0  1
  KCNN3 MUTATED    3  4
  KCNN3 WILD-TYPE 31  2
  KCNN3 MUTATED KCNN3 WILD-TYPE 
              7              33 
  KCNN3 MUTATED KCNN3 WILD-TYPE 
              4               2 
$`KCNN3 MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FF-8043 TCGA-FF-8047 
       23.28         1.91        24.62         8.15        31.73         4.14 
TCGA-GS-A9U4 
       12.85 

$`KCNN3 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A7DS TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 
        4.34         4.34        23.64        14.04        18.18        35.54 
TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       31.10        24.69        27.35        22.32         9.80        10.29 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D4 
       26.01        12.66        31.96        41.16        98.07        51.98 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU 
       42.71        43.86        57.17        32.28        38.24       128.12 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 
       24.00        53.16        45.14       109.58        25.15       111.58 
TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.91         0.03         0.56 

  KCNN3 MUTATED KCNN3 WILD-TYPE 
           1.91            0.03 
  KCNN3 MUTATED KCNN3 WILD-TYPE 
          31.73          128.12 
  KCNN3 MUTATED KCNN3 WILD-TYPE 
          12.85           27.35 
[1] "1.9 - 31.7 (12.8)"  "0.0 - 128.1 (27.4)"
[1] "hr=" "25" 
D59V2, continuous
D59V3, binary
                 cls
clus               0  1
  KCNN3 MUTATED    5  2
  KCNN3 WILD-TYPE 19 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED      5    2
  KCNN3 WILD-TYPE   19   14
        clus
vv       KCNN3 MUTATED KCNN3 WILD-TYPE
  FEMALE             5              19
  MALE               2              14
[1] 2 2
[1] FALSE
D59V4, binary
                 cls
clus               0  1
  KCNN3 MUTATED    7  0
  KCNN3 WILD-TYPE 26  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED      7    0
  KCNN3 WILD-TYPE   26    6
     clus
vv    KCNN3 MUTATED KCNN3 WILD-TYPE
  NO              7              26
  YES             0               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  KCNN3 MUTATED                                                                                   7
  KCNN3 WILD-TYPE                                                                                26
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  KCNN3 MUTATED                          0                                  0
  KCNN3 WILD-TYPE                        3                                  4
D59V5, multiclass
                                                                                   clus
vv                                                                                  KCNN3 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             7
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  KCNN3 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              26
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KCNN3 MUTATED       6                         0     1
  KCNN3 WILD-TYPE    12                         1    20
D59V6, multiclass
                           clus
vv                          KCNN3 MUTATED KCNN3 WILD-TYPE
  ASIAN                                 6              12
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 1              20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                 cls
clus               0  1
  KCNN3 MUTATED    1  6
  KCNN3 WILD-TYPE 11 22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN3 MUTATED      1    6
  KCNN3 WILD-TYPE   11   22
                        clus
vv                       KCNN3 MUTATED KCNN3 WILD-TYPE
  HISPANIC OR LATINO                 1              11
  NOT HISPANIC OR LATINO             6              22
[1] 2 2
[1] FALSE

Clustering(60) Variable = RNASEH2B MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  RNASEH2B MUTATED    3  0
  RNASEH2B WILD-TYPE 31  6
  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
                 3                 37 
  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
                 0                  6 
$`RNASEH2B MUTATED`
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-GS-A9TU 
       26.01        12.66       128.12 

$`RNASEH2B WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       24.69         4.14        27.35        22.32         9.80        10.29 
TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
       31.96        41.16        98.07        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       57.17        32.28        38.24        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
             12.66               0.03 
  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
            128.12             111.58 
  RNASEH2B MUTATED RNASEH2B WILD-TYPE 
             26.01              25.15 
[1] "12.7 - 128.1 (26.0)" "0.0 - 111.6 (25.1)" 
[1] "hr="     "7.5e+07"
D60V2, continuous
D60V3, binary
                    cls
clus                  0  1
  RNASEH2B MUTATED    0  3
  RNASEH2B WILD-TYPE 24 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RNASEH2B MUTATED      0    3
  RNASEH2B WILD-TYPE   24   13
        clus
vv       RNASEH2B MUTATED RNASEH2B WILD-TYPE
  FEMALE                0                 24
  MALE                  3                 13
[1] 2 2
[1] FALSE
D60V4, binary
                    cls
clus                  0  1
  RNASEH2B MUTATED    2  1
  RNASEH2B WILD-TYPE 31  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RNASEH2B MUTATED      2    1
  RNASEH2B WILD-TYPE   31    5
     clus
vv    RNASEH2B MUTATED RNASEH2B WILD-TYPE
  NO                 2                 31
  YES                1                  5
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  RNASEH2B MUTATED                                                                                   3
  RNASEH2B WILD-TYPE                                                                                30
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  RNASEH2B MUTATED                          0
  RNASEH2B WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  RNASEH2B MUTATED                                    0
  RNASEH2B WILD-TYPE                                  4
D60V5, multiclass
                                                                                   clus
vv                                                                                  RNASEH2B MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                3
  PRIMARY DLBCL OF THE CNS                                                                         0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               0
                                                                                   clus
vv                                                                                  RNASEH2B WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 30
  PRIMARY DLBCL OF THE CNS                                                                           3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RNASEH2B MUTATED       2                         0     1
  RNASEH2B WILD-TYPE    16                         1    20
D60V6, multiclass
                           clus
vv                          RNASEH2B MUTATED RNASEH2B WILD-TYPE
  ASIAN                                    2                 16
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    1                 20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                    cls
clus                  0  1
  RNASEH2B MUTATED    1  2
  RNASEH2B WILD-TYPE 11 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RNASEH2B MUTATED      1    2
  RNASEH2B WILD-TYPE   11   26
                        clus
vv                       RNASEH2B MUTATED RNASEH2B WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO                2                 26
[1] 2 2
[1] FALSE

Clustering(61) Variable = OTOP1 MUTATION ANALYSIS
D61V1, survival
                 sevent
clus2              0  1
  OTOP1 MUTATED    2  2
  OTOP1 WILD-TYPE 32  4
  OTOP1 MUTATED OTOP1 WILD-TYPE 
              4              36 
  OTOP1 MUTATED OTOP1 WILD-TYPE 
              2               4 
$`OTOP1 MUTATED`
TCGA-FA-A6HN TCGA-FA-A7Q1 TCGA-FF-8042 TCGA-GR-A4D6 
        1.91         8.15        31.10        43.86 

$`OTOP1 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A82F 
        4.34         4.34        23.28        24.62        23.64        14.04 
TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       18.18        35.54        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       41.16        98.07        51.98        42.71        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  OTOP1 MUTATED OTOP1 WILD-TYPE 
           1.91            0.03 
  OTOP1 MUTATED OTOP1 WILD-TYPE 
          43.86          128.12 
  OTOP1 MUTATED OTOP1 WILD-TYPE 
         19.625          25.530 
[1] "1.9 - 43.9 (19.6)"  "0.0 - 128.1 (25.5)"
[1] "hr=" "5.7"
D61V2, continuous
D61V3, binary
                 cls
clus               0  1
  OTOP1 MUTATED    3  1
  OTOP1 WILD-TYPE 21 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTOP1 MUTATED      3    1
  OTOP1 WILD-TYPE   21   15
        clus
vv       OTOP1 MUTATED OTOP1 WILD-TYPE
  FEMALE             3              21
  MALE               1              15
[1] 2 2
[1] FALSE
D61V4, binary
                 cls
clus               0  1
  OTOP1 MUTATED    4  0
  OTOP1 WILD-TYPE 29  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTOP1 MUTATED      4    0
  OTOP1 WILD-TYPE   29    6
     clus
vv    OTOP1 MUTATED OTOP1 WILD-TYPE
  NO              4              29
  YES             0               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  OTOP1 MUTATED                                                                                   4
  OTOP1 WILD-TYPE                                                                                29
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  OTOP1 MUTATED                          0                                  0
  OTOP1 WILD-TYPE                        3                                  4
D61V5, multiclass
                                                                                   clus
vv                                                                                  OTOP1 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             4
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  OTOP1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              29
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OTOP1 MUTATED       4                         0     0
  OTOP1 WILD-TYPE    14                         1    21
D61V6, multiclass
                           clus
vv                          OTOP1 MUTATED OTOP1 WILD-TYPE
  ASIAN                                 4              14
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 0              21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                 cls
clus               0  1
  OTOP1 MUTATED    0  4
  OTOP1 WILD-TYPE 12 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTOP1 MUTATED      0    4
  OTOP1 WILD-TYPE   12   24
                        clus
vv                       OTOP1 MUTATED OTOP1 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             4              24
[1] 2 2
[1] FALSE

Clustering(62) Variable = AATK MUTATION ANALYSIS
D62V1, survival
                sevent
clus2             0  1
  AATK MUTATED    1  2
  AATK WILD-TYPE 33  4
  AATK MUTATED AATK WILD-TYPE 
             3             37 
  AATK MUTATED AATK WILD-TYPE 
             2              4 
$`AATK MUTATED`
TCGA-FA-A4XK TCGA-FM-8000 TCGA-G8-6324 
       23.28        31.96        41.16 

$`AATK WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         1.91        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       12.66        98.07        51.98        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       32.28        38.24       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  AATK MUTATED AATK WILD-TYPE 
         23.28           0.03 
  AATK MUTATED AATK WILD-TYPE 
         41.16         128.12 
  AATK MUTATED AATK WILD-TYPE 
         31.96          25.15 
[1] "23.3 - 41.2 (32.0)" "0.0 - 128.1 (25.1)"
[1] "hr=" "4.8"
D62V2, continuous
D62V3, binary
                cls
clus              0  1
  AATK MUTATED    2  1
  AATK WILD-TYPE 22 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  AATK MUTATED      2    1
  AATK WILD-TYPE   22   15
        clus
vv       AATK MUTATED AATK WILD-TYPE
  FEMALE            2             22
  MALE              1             15
[1] 2 2
[1] FALSE
D62V4, binary
                cls
clus              0  1
  AATK MUTATED    3  0
  AATK WILD-TYPE 30  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  AATK MUTATED      3    0
  AATK WILD-TYPE   30    6
     clus
vv    AATK MUTATED AATK WILD-TYPE
  NO             3             30
  YES            0              6
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  AATK MUTATED                                                                                   3
  AATK WILD-TYPE                                                                                30
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  AATK MUTATED                          0                                  0
  AATK WILD-TYPE                        3                                  4
D62V5, multiclass
                                                                                   clus
vv                                                                                  AATK MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)            3
  PRIMARY DLBCL OF THE CNS                                                                     0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                           0
                                                                                   clus
vv                                                                                  AATK WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             30
  PRIMARY DLBCL OF THE CNS                                                                       3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AATK MUTATED       1                         1     1
  AATK WILD-TYPE    17                         0    20
D62V6, multiclass
                           clus
vv                          AATK MUTATED AATK WILD-TYPE
  ASIAN                                1             17
  BLACK OR AFRICAN AMERICAN            1              0
  WHITE                                1             20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                cls
clus              0  1
  AATK MUTATED    0  3
  AATK WILD-TYPE 12 25
[1] "tbl2"
                cls
clus             [,1] [,2]
  AATK MUTATED      0    3
  AATK WILD-TYPE   12   25
                        clus
vv                       AATK MUTATED AATK WILD-TYPE
  HISPANIC OR LATINO                0             12
  NOT HISPANIC OR LATINO            3             25
[1] 2 2
[1] FALSE

Clustering(63) Variable = ARID1A MUTATION ANALYSIS
D63V1, survival
                  sevent
clus2               0  1
  ARID1A MUTATED    4  1
  ARID1A WILD-TYPE 30  5
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               35 
  ARID1A MUTATED ARID1A WILD-TYPE 
               1                5 
$`ARID1A MUTATED`
TCGA-FA-A86F TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-A4D4 TCGA-GR-A4D9 
       18.18        31.96        41.16        51.98        57.17 

$`ARID1A WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
        8.15        14.04        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GS-A9TQ TCGA-GS-A9TT 
       12.66        98.07        42.71        43.86        32.28        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
      128.12        24.00        53.16        45.14       109.58        25.15 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
      111.58        12.85        25.91         0.03         0.56 

  ARID1A MUTATED ARID1A WILD-TYPE 
           18.18             0.03 
  ARID1A MUTATED ARID1A WILD-TYPE 
           57.17           128.12 
  ARID1A MUTATED ARID1A WILD-TYPE 
           41.16            24.69 
[1] "18.2 - 57.2 (41.2)" "0.0 - 128.1 (24.7)"
[1] "hr=" "1"  
D63V2, continuous
D63V3, binary
                  cls
clus                0  1
  ARID1A MUTATED    5  0
  ARID1A WILD-TYPE 19 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      5    0
  ARID1A WILD-TYPE   19   16
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              5               19
  MALE                0               16
[1] 2 2
[1] FALSE
D63V4, binary
                  cls
clus                0  1
  ARID1A MUTATED    5  0
  ARID1A WILD-TYPE 28  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      5    0
  ARID1A WILD-TYPE   28    6
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO               5               28
  YES              0                6
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  ARID1A MUTATED                                                                                   5
  ARID1A WILD-TYPE                                                                                28
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  ARID1A MUTATED                          0                                  0
  ARID1A WILD-TYPE                        3                                  4
D63V5, multiclass
                                                                                   clus
vv                                                                                  ARID1A MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              5
  PRIMARY DLBCL OF THE CNS                                                                       0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             0
                                                                                   clus
vv                                                                                  ARID1A WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               28
  PRIMARY DLBCL OF THE CNS                                                                         3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED       0                         1     4
  ARID1A WILD-TYPE    18                         0    17
D63V6, multiclass
                           clus
vv                          ARID1A MUTATED ARID1A WILD-TYPE
  ASIAN                                  0               18
  BLACK OR AFRICAN AMERICAN              1                0
  WHITE                                  4               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                  cls
clus                0  1
  ARID1A MUTATED    0  5
  ARID1A WILD-TYPE 12 23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      0    5
  ARID1A WILD-TYPE   12   23
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              5               23
[1] 2 2
[1] FALSE

Clustering(64) Variable = GUCA1C MUTATION ANALYSIS
D64V1, survival
                  sevent
clus2               0  1
  GUCA1C MUTATED    1  2
  GUCA1C WILD-TYPE 33  4
  GUCA1C MUTATED GUCA1C WILD-TYPE 
               3               37 
  GUCA1C MUTATED GUCA1C WILD-TYPE 
               2                4 
$`GUCA1C MUTATED`
TCGA-FA-A4XK TCGA-G8-6324 TCGA-GR-7353 
       23.28        41.16        98.07 

$`GUCA1C WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         1.91        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       12.66        31.96        51.98        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       32.28        38.24       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  GUCA1C MUTATED GUCA1C WILD-TYPE 
           23.28             0.03 
  GUCA1C MUTATED GUCA1C WILD-TYPE 
           98.07           128.12 
  GUCA1C MUTATED GUCA1C WILD-TYPE 
           41.16            25.15 
[1] "23.3 - 98.1 (41.2)" "0.0 - 128.1 (25.1)"
[1] "hr=" "4.2"
D64V2, continuous
D64V3, binary
                  cls
clus                0  1
  GUCA1C MUTATED    1  2
  GUCA1C WILD-TYPE 23 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCA1C MUTATED      1    2
  GUCA1C WILD-TYPE   23   14
        clus
vv       GUCA1C MUTATED GUCA1C WILD-TYPE
  FEMALE              1               23
  MALE                2               14
[1] 2 2
[1] FALSE
D64V4, binary
                  cls
clus                0  1
  GUCA1C MUTATED    3  0
  GUCA1C WILD-TYPE 30  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCA1C MUTATED      3    0
  GUCA1C WILD-TYPE   30    6
     clus
vv    GUCA1C MUTATED GUCA1C WILD-TYPE
  NO               3               30
  YES              0                6
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  GUCA1C MUTATED                                                                                   3
  GUCA1C WILD-TYPE                                                                                30
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  GUCA1C MUTATED                          0                                  0
  GUCA1C WILD-TYPE                        3                                  4
D64V5, multiclass
                                                                                   clus
vv                                                                                  GUCA1C MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              3
  PRIMARY DLBCL OF THE CNS                                                                       0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             0
                                                                                   clus
vv                                                                                  GUCA1C WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               30
  PRIMARY DLBCL OF THE CNS                                                                         3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GUCA1C MUTATED       1                         1     1
  GUCA1C WILD-TYPE    17                         0    20
D64V6, multiclass
                           clus
vv                          GUCA1C MUTATED GUCA1C WILD-TYPE
  ASIAN                                  1               17
  BLACK OR AFRICAN AMERICAN              1                0
  WHITE                                  1               20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                  cls
clus                0  1
  GUCA1C MUTATED    0  3
  GUCA1C WILD-TYPE 12 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCA1C MUTATED      0    3
  GUCA1C WILD-TYPE   12   25
                        clus
vv                       GUCA1C MUTATED GUCA1C WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              3               25
[1] 2 2
[1] FALSE

Clustering(65) Variable = TRIM48 MUTATION ANALYSIS
D65V1, survival
                  sevent
clus2               0  1
  TRIM48 MUTATED    5  3
  TRIM48 WILD-TYPE 29  3
  TRIM48 MUTATED TRIM48 WILD-TYPE 
               8               32 
  TRIM48 MUTATED TRIM48 WILD-TYPE 
               3                3 
$`TRIM48 MUTATED`
TCGA-FA-A7Q1 TCGA-FF-8046 TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FM-8000 TCGA-G8-6324 
        8.15        24.69        10.29        26.01        31.96        41.16 
TCGA-GS-A9TT TCGA-GS-A9TV 
       38.24        24.00 

$`TRIM48 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 
       14.04        18.18        35.54        31.10        31.73         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CX TCGA-GR-7353 TCGA-GR-A4D4 
       27.35        22.32         9.80        12.66        98.07        51.98 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TU TCGA-GS-A9TW 
       42.71        43.86        57.17        32.28       128.12        53.16 
TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N 
       45.14       109.58        25.15       111.58        12.85        25.91 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  TRIM48 MUTATED TRIM48 WILD-TYPE 
            8.15             0.03 
  TRIM48 MUTATED TRIM48 WILD-TYPE 
           41.16           128.12 
  TRIM48 MUTATED TRIM48 WILD-TYPE 
           25.35            25.53 
[1] "8.2 - 41.2 (25.4)"  "0.0 - 128.1 (25.5)"
[1] "hr=" "4.2"
D65V2, continuous
D65V3, binary
                  cls
clus                0  1
  TRIM48 MUTATED    4  4
  TRIM48 WILD-TYPE 20 12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM48 MUTATED      4    4
  TRIM48 WILD-TYPE   20   12
        clus
vv       TRIM48 MUTATED TRIM48 WILD-TYPE
  FEMALE              4               20
  MALE                4               12
[1] 2 2
[1] FALSE
D65V4, binary
                  cls
clus                0  1
  TRIM48 MUTATED    6  2
  TRIM48 WILD-TYPE 27  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM48 MUTATED      6    2
  TRIM48 WILD-TYPE   27    4
     clus
vv    TRIM48 MUTATED TRIM48 WILD-TYPE
  NO               6               27
  YES              2                4
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  TRIM48 MUTATED                                                                                   7
  TRIM48 WILD-TYPE                                                                                26
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  TRIM48 MUTATED                          0                                  1
  TRIM48 WILD-TYPE                        3                                  3
D65V5, multiclass
                                                                                   clus
vv                                                                                  TRIM48 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              7
  PRIMARY DLBCL OF THE CNS                                                                       0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             1
                                                                                   clus
vv                                                                                  TRIM48 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               26
  PRIMARY DLBCL OF THE CNS                                                                         3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TRIM48 MUTATED       4                         1     3
  TRIM48 WILD-TYPE    14                         0    18
D65V6, multiclass
                           clus
vv                          TRIM48 MUTATED TRIM48 WILD-TYPE
  ASIAN                                  4               14
  BLACK OR AFRICAN AMERICAN              1                0
  WHITE                                  3               18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                  cls
clus                0  1
  TRIM48 MUTATED    2  6
  TRIM48 WILD-TYPE 10 22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM48 MUTATED      2    6
  TRIM48 WILD-TYPE   10   22
                        clus
vv                       TRIM48 MUTATED TRIM48 WILD-TYPE
  HISPANIC OR LATINO                  2               10
  NOT HISPANIC OR LATINO              6               22
[1] 2 2
[1] FALSE

Clustering(66) Variable = CSGALNACT2 MUTATION ANALYSIS
D66V1, survival
                      sevent
clus2                   0  1
  CSGALNACT2 MUTATED    3  2
  CSGALNACT2 WILD-TYPE 31  4
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   5                   35 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   2                    4 
$`CSGALNACT2 MUTATED`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8043 TCGA-G8-6324 TCGA-GR-A4D5 
       23.28        35.54        31.73        41.16        42.71 

$`CSGALNACT2 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         1.91        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       14.04        18.18        31.10        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT 
       98.07        51.98        43.86        57.17        32.28        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
      128.12        24.00        53.16        45.14       109.58        25.15 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
      111.58        12.85        25.91         0.03         0.56 

  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
               23.28                 0.03 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
               42.71               128.12 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
               35.54                24.69 
[1] "23.3 - 42.7 (35.5)" "0.0 - 128.1 (24.7)"
[1] "hr=" "2.6"
D66V2, continuous
D66V3, binary
                      cls
clus                    0  1
  CSGALNACT2 MUTATED    4  1
  CSGALNACT2 WILD-TYPE 20 15
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      4    1
  CSGALNACT2 WILD-TYPE   20   15
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  FEMALE                  4                   20
  MALE                    1                   15
[1] 2 2
[1] FALSE
D66V4, binary
                      cls
clus                    0  1
  CSGALNACT2 MUTATED    5  0
  CSGALNACT2 WILD-TYPE 28  6
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      5    0
  CSGALNACT2 WILD-TYPE   28    6
     clus
vv    CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  NO                   5                   28
  YES                  0                    6
[1] 2 2
[1] FALSE
                      vv
clus                   DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  CSGALNACT2 MUTATED                                                                                   4
  CSGALNACT2 WILD-TYPE                                                                                29
                      vv
clus                   PRIMARY DLBCL OF THE CNS
  CSGALNACT2 MUTATED                          0
  CSGALNACT2 WILD-TYPE                        3
                      vv
clus                   PRIMARY MEDIASTINAL (THYMIC) DLBCL
  CSGALNACT2 MUTATED                                    1
  CSGALNACT2 WILD-TYPE                                  3
D66V5, multiclass
                                                                                   clus
vv                                                                                  CSGALNACT2 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                  4
  PRIMARY DLBCL OF THE CNS                                                                           0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 1
                                                                                   clus
vv                                                                                  CSGALNACT2 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                   29
  PRIMARY DLBCL OF THE CNS                                                                             3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                   3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                   ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CSGALNACT2 MUTATED       3                         1     1
  CSGALNACT2 WILD-TYPE    15                         0    20
D66V6, multiclass
                           clus
vv                          CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  ASIAN                                      3                   15
  BLACK OR AFRICAN AMERICAN                  1                    0
  WHITE                                      1                   20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                      cls
clus                    0  1
  CSGALNACT2 MUTATED    0  5
  CSGALNACT2 WILD-TYPE 12 23
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      0    5
  CSGALNACT2 WILD-TYPE   12   23
                        clus
vv                       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  HISPANIC OR LATINO                      0                   12
  NOT HISPANIC OR LATINO                  5                   23
[1] 2 2
[1] FALSE

Clustering(67) Variable = CRIPAK MUTATION ANALYSIS
D67V1, survival
                  sevent
clus2               0  1
  CRIPAK MUTATED    5  1
  CRIPAK WILD-TYPE 29  5
  CRIPAK MUTATED CRIPAK WILD-TYPE 
               6               34 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
               1                5 
$`CRIPAK MUTATED`
TCGA-FA-A4BB TCGA-FF-8062 TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
        4.34        22.32        41.16        98.07        51.98        42.71 

$`CRIPAK WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34        23.28         1.91        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
        4.14        27.35         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU 
       31.96        43.86        57.17        32.28        38.24       128.12 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 
       24.00        53.16        45.14       109.58        25.15       111.58 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85        25.91         0.03         0.56 

  CRIPAK MUTATED CRIPAK WILD-TYPE 
            4.34             0.03 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
           98.07           128.12 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
          41.935           24.920 
[1] "4.3 - 98.1 (41.9)"  "0.0 - 128.1 (24.9)"
[1] "hr=" "1.2"
D67V2, continuous
D67V3, binary
                  cls
clus                0  1
  CRIPAK MUTATED    4  2
  CRIPAK WILD-TYPE 20 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED      4    2
  CRIPAK WILD-TYPE   20   14
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  FEMALE              4               20
  MALE                2               14
[1] 2 2
[1] FALSE
D67V4, binary
                  cls
clus                0  1
  CRIPAK MUTATED    6  0
  CRIPAK WILD-TYPE 27  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED      6    0
  CRIPAK WILD-TYPE   27    6
     clus
vv    CRIPAK MUTATED CRIPAK WILD-TYPE
  NO               6               27
  YES              0                6
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  CRIPAK MUTATED                                                                                   6
  CRIPAK WILD-TYPE                                                                                27
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  CRIPAK MUTATED                          0                                  0
  CRIPAK WILD-TYPE                        3                                  4
D67V5, multiclass
                                                                                   clus
vv                                                                                  CRIPAK MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              6
  PRIMARY DLBCL OF THE CNS                                                                       0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             0
                                                                                   clus
vv                                                                                  CRIPAK WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               27
  PRIMARY DLBCL OF THE CNS                                                                         3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CRIPAK MUTATED       1                         1     4
  CRIPAK WILD-TYPE    17                         0    17
D67V6, multiclass
                           clus
vv                          CRIPAK MUTATED CRIPAK WILD-TYPE
  ASIAN                                  1               17
  BLACK OR AFRICAN AMERICAN              1                0
  WHITE                                  4               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                  cls
clus                0  1
  CRIPAK MUTATED    0  6
  CRIPAK WILD-TYPE 12 22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED      0    6
  CRIPAK WILD-TYPE   12   22
                        clus
vv                       CRIPAK MUTATED CRIPAK WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              6               22
[1] 2 2
[1] FALSE

Clustering(68) Variable = DHRS4 MUTATION ANALYSIS
D68V1, survival
                 sevent
clus2              0  1
  DHRS4 MUTATED    2  2
  DHRS4 WILD-TYPE 32  4
  DHRS4 MUTATED DHRS4 WILD-TYPE 
              4              36 
  DHRS4 MUTATED DHRS4 WILD-TYPE 
              2               4 
$`DHRS4 MUTATED`
TCGA-FA-A6HN TCGA-FA-A6HO TCGA-G8-6324 TCGA-GR-7353 
        1.91        24.62        41.16        98.07 

$`DHRS4 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34         4.34        23.28        23.64         8.15        14.04 
TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       18.18        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       31.96        51.98        42.71        43.86        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  DHRS4 MUTATED DHRS4 WILD-TYPE 
           1.91            0.03 
  DHRS4 MUTATED DHRS4 WILD-TYPE 
          98.07          128.12 
  DHRS4 MUTATED DHRS4 WILD-TYPE 
          32.89           25.53 
[1] "1.9 - 98.1 (32.9)"  "0.0 - 128.1 (25.5)"
[1] "hr=" "4"  
D68V2, continuous
D68V3, binary
                 cls
clus               0  1
  DHRS4 MUTATED    2  2
  DHRS4 WILD-TYPE 22 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS4 MUTATED      2    2
  DHRS4 WILD-TYPE   22   14
        clus
vv       DHRS4 MUTATED DHRS4 WILD-TYPE
  FEMALE             2              22
  MALE               2              14
[1] 2 2
[1] FALSE
D68V4, binary
                 cls
clus               0  1
  DHRS4 MUTATED    4  0
  DHRS4 WILD-TYPE 29  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS4 MUTATED      4    0
  DHRS4 WILD-TYPE   29    6
     clus
vv    DHRS4 MUTATED DHRS4 WILD-TYPE
  NO              4              29
  YES             0               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DHRS4 MUTATED                                                                                   4
  DHRS4 WILD-TYPE                                                                                29
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DHRS4 MUTATED                          0                                  0
  DHRS4 WILD-TYPE                        3                                  4
D68V5, multiclass
                                                                                   clus
vv                                                                                  DHRS4 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             4
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  DHRS4 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              29
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DHRS4 MUTATED       2                         1     1
  DHRS4 WILD-TYPE    16                         0    20
D68V6, multiclass
                           clus
vv                          DHRS4 MUTATED DHRS4 WILD-TYPE
  ASIAN                                 2              16
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 1              20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                 cls
clus               0  1
  DHRS4 MUTATED    0  4
  DHRS4 WILD-TYPE 12 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS4 MUTATED      0    4
  DHRS4 WILD-TYPE   12   24
                        clus
vv                       DHRS4 MUTATED DHRS4 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             4              24
[1] 2 2
[1] FALSE

Clustering(69) Variable = FAM21A MUTATION ANALYSIS
D69V1, survival
                  sevent
clus2               0  1
  FAM21A MUTATED    2  2
  FAM21A WILD-TYPE 32  4
  FAM21A MUTATED FAM21A WILD-TYPE 
               4               36 
  FAM21A MUTATED FAM21A WILD-TYPE 
               2                4 
$`FAM21A MUTATED`
TCGA-FF-A7CR TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D5 
       10.29        41.16        98.07        42.71 

$`FAM21A WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CW 
       24.69         4.14        27.35        22.32         9.80        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       12.66        31.96        51.98        43.86        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  FAM21A MUTATED FAM21A WILD-TYPE 
           10.29             0.03 
  FAM21A MUTATED FAM21A WILD-TYPE 
           98.07           128.12 
  FAM21A MUTATED FAM21A WILD-TYPE 
          41.935           24.920 
[1] "10.3 - 98.1 (41.9)" "0.0 - 128.1 (24.9)"
[1] "hr=" "3.2"
D69V2, continuous
D69V3, binary
                  cls
clus                0  1
  FAM21A MUTATED    2  2
  FAM21A WILD-TYPE 22 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM21A MUTATED      2    2
  FAM21A WILD-TYPE   22   14
        clus
vv       FAM21A MUTATED FAM21A WILD-TYPE
  FEMALE              2               22
  MALE                2               14
[1] 2 2
[1] FALSE
D69V4, binary
                  cls
clus                0  1
  FAM21A MUTATED    4  0
  FAM21A WILD-TYPE 29  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM21A MUTATED      4    0
  FAM21A WILD-TYPE   29    6
     clus
vv    FAM21A MUTATED FAM21A WILD-TYPE
  NO               4               29
  YES              0                6
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  FAM21A MUTATED                                                                                   4
  FAM21A WILD-TYPE                                                                                29
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  FAM21A MUTATED                          0                                  0
  FAM21A WILD-TYPE                        3                                  4
D69V5, multiclass
                                                                                   clus
vv                                                                                  FAM21A MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              4
  PRIMARY DLBCL OF THE CNS                                                                       0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             0
                                                                                   clus
vv                                                                                  FAM21A WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               29
  PRIMARY DLBCL OF THE CNS                                                                         3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM21A MUTATED       1                         1     2
  FAM21A WILD-TYPE    17                         0    19
D69V6, multiclass
                           clus
vv                          FAM21A MUTATED FAM21A WILD-TYPE
  ASIAN                                  1               17
  BLACK OR AFRICAN AMERICAN              1                0
  WHITE                                  2               19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                  cls
clus                0  1
  FAM21A MUTATED    0  4
  FAM21A WILD-TYPE 12 24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM21A MUTATED      0    4
  FAM21A WILD-TYPE   12   24
                        clus
vv                       FAM21A MUTATED FAM21A WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              4               24
[1] 2 2
[1] FALSE

Clustering(70) Variable = KIAA1529 MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  KIAA1529 MUTATED    3  1
  KIAA1529 WILD-TYPE 31  5
  KIAA1529 MUTATED KIAA1529 WILD-TYPE 
                 4                 36 
  KIAA1529 MUTATED KIAA1529 WILD-TYPE 
                 1                  5 
$`KIAA1529 MUTATED`
TCGA-FF-A7CX TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D9 
       12.66        41.16        98.07        57.17 

$`KIAA1529 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       24.69         4.14        27.35        22.32         9.80        10.29 
TCGA-FF-A7CW TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GS-A9TQ 
       26.01        31.96        51.98        42.71        43.86        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  KIAA1529 MUTATED KIAA1529 WILD-TYPE 
             12.66               0.03 
  KIAA1529 MUTATED KIAA1529 WILD-TYPE 
             98.07             128.12 
  KIAA1529 MUTATED KIAA1529 WILD-TYPE 
            49.165             24.920 
[1] "12.7 - 98.1 (49.2)" "0.0 - 128.1 (24.9)"
[1] "hr=" "1.2"
D70V2, continuous
D70V3, binary
                    cls
clus                  0  1
  KIAA1529 MUTATED    2  2
  KIAA1529 WILD-TYPE 22 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1529 MUTATED      2    2
  KIAA1529 WILD-TYPE   22   14
        clus
vv       KIAA1529 MUTATED KIAA1529 WILD-TYPE
  FEMALE                2                 22
  MALE                  2                 14
[1] 2 2
[1] FALSE
D70V4, binary
                    cls
clus                  0  1
  KIAA1529 MUTATED    4  0
  KIAA1529 WILD-TYPE 29  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1529 MUTATED      4    0
  KIAA1529 WILD-TYPE   29    6
     clus
vv    KIAA1529 MUTATED KIAA1529 WILD-TYPE
  NO                 4                 29
  YES                0                  6
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  KIAA1529 MUTATED                                                                                   4
  KIAA1529 WILD-TYPE                                                                                29
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  KIAA1529 MUTATED                          0
  KIAA1529 WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  KIAA1529 MUTATED                                    0
  KIAA1529 WILD-TYPE                                  4
D70V5, multiclass
                                                                                   clus
vv                                                                                  KIAA1529 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                4
  PRIMARY DLBCL OF THE CNS                                                                         0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               0
                                                                                   clus
vv                                                                                  KIAA1529 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 29
  PRIMARY DLBCL OF THE CNS                                                                           3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1529 MUTATED       1                         1     2
  KIAA1529 WILD-TYPE    17                         0    19
D70V6, multiclass
                           clus
vv                          KIAA1529 MUTATED KIAA1529 WILD-TYPE
  ASIAN                                    1                 17
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                    2                 19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                    cls
clus                  0  1
  KIAA1529 MUTATED    0  4
  KIAA1529 WILD-TYPE 12 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1529 MUTATED      0    4
  KIAA1529 WILD-TYPE   12   24
                        clus
vv                       KIAA1529 MUTATED KIAA1529 WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                4                 24
[1] 2 2
[1] FALSE

Clustering(71) Variable = OR2M5 MUTATION ANALYSIS
D71V1, survival
                 sevent
clus2              0  1
  OR2M5 MUTATED    4  0
  OR2M5 WILD-TYPE 30  6
  OR2M5 MUTATED OR2M5 WILD-TYPE 
              4              36 
  OR2M5 MUTATED OR2M5 WILD-TYPE 
              0               6 
$`OR2M5 MUTATED`
TCGA-FA-8693 TCGA-FA-A82F TCGA-FF-8061 TCGA-GR-A4D9 
        4.34        14.04        27.35        57.17 

$`OR2M5 WILD-TYPE`
TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34        23.28         1.91        24.62        23.64         8.15 
TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       18.18        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GS-A9TQ 
       41.16        98.07        51.98        42.71        43.86        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  OR2M5 MUTATED OR2M5 WILD-TYPE 
           4.34            0.03 
  OR2M5 MUTATED OR2M5 WILD-TYPE 
          57.17          128.12 
  OR2M5 MUTATED OR2M5 WILD-TYPE 
         20.695          25.530 
[1] "4.3 - 57.2 (20.7)"  "0.0 - 128.1 (25.5)"
[1] "hr="     "7.7e+07"
D71V2, continuous
D71V3, binary
                 cls
clus               0  1
  OR2M5 MUTATED    2  2
  OR2M5 WILD-TYPE 22 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M5 MUTATED      2    2
  OR2M5 WILD-TYPE   22   14
        clus
vv       OR2M5 MUTATED OR2M5 WILD-TYPE
  FEMALE             2              22
  MALE               2              14
[1] 2 2
[1] FALSE
D71V4, binary
                 cls
clus               0  1
  OR2M5 MUTATED    4  0
  OR2M5 WILD-TYPE 29  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M5 MUTATED      4    0
  OR2M5 WILD-TYPE   29    6
     clus
vv    OR2M5 MUTATED OR2M5 WILD-TYPE
  NO              4              29
  YES             0               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  OR2M5 MUTATED                                                                                   4
  OR2M5 WILD-TYPE                                                                                29
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  OR2M5 MUTATED                          0                                  0
  OR2M5 WILD-TYPE                        3                                  4
D71V5, multiclass
                                                                                   clus
vv                                                                                  OR2M5 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             4
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  OR2M5 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              29
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR2M5 MUTATED       2                         0     2
  OR2M5 WILD-TYPE    16                         1    19
D71V6, multiclass
                           clus
vv                          OR2M5 MUTATED OR2M5 WILD-TYPE
  ASIAN                                 2              16
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 2              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                 cls
clus               0  1
  OR2M5 MUTATED    0  4
  OR2M5 WILD-TYPE 12 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M5 MUTATED      0    4
  OR2M5 WILD-TYPE   12   24
                        clus
vv                       OR2M5 MUTATED OR2M5 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             4              24
[1] 2 2
[1] FALSE

Clustering(72) Variable = KRT6A MUTATION ANALYSIS
D72V1, survival
                 sevent
clus2              0  1
  KRT6A MUTATED    3  1
  KRT6A WILD-TYPE 31  5
  KRT6A MUTATED KRT6A WILD-TYPE 
              4              36 
  KRT6A MUTATED KRT6A WILD-TYPE 
              1               5 
$`KRT6A MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FF-8047 
       23.28        24.62        23.64         4.14 

$`KRT6A WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F 
        4.34         4.34         1.91         8.15        14.04        18.18 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.10        31.73        24.69        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66        31.96        41.16 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       98.07        51.98        42.71        43.86        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  KRT6A MUTATED KRT6A WILD-TYPE 
           4.14            0.03 
  KRT6A MUTATED KRT6A WILD-TYPE 
          24.62          128.12 
  KRT6A MUTATED KRT6A WILD-TYPE 
          23.46           26.68 
[1] "4.1 - 24.6 (23.5)"  "0.0 - 128.1 (26.7)"
[1] "hr=" "2.2"
D72V2, continuous
D72V3, binary
                 cls
clus               0  1
  KRT6A MUTATED    3  1
  KRT6A WILD-TYPE 21 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT6A MUTATED      3    1
  KRT6A WILD-TYPE   21   15
        clus
vv       KRT6A MUTATED KRT6A WILD-TYPE
  FEMALE             3              21
  MALE               1              15
[1] 2 2
[1] FALSE
D72V4, binary
                 cls
clus               0  1
  KRT6A MUTATED    4  0
  KRT6A WILD-TYPE 29  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT6A MUTATED      4    0
  KRT6A WILD-TYPE   29    6
     clus
vv    KRT6A MUTATED KRT6A WILD-TYPE
  NO              4              29
  YES             0               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  KRT6A MUTATED                                                                                   4
  KRT6A WILD-TYPE                                                                                29
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  KRT6A MUTATED                          0                                  0
  KRT6A WILD-TYPE                        3                                  4
D72V5, multiclass
                                                                                   clus
vv                                                                                  KRT6A MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             4
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  KRT6A WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              29
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRT6A MUTATED       4                         0     0
  KRT6A WILD-TYPE    14                         1    21
D72V6, multiclass
                           clus
vv                          KRT6A MUTATED KRT6A WILD-TYPE
  ASIAN                                 4              14
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 0              21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                 cls
clus               0  1
  KRT6A MUTATED    0  4
  KRT6A WILD-TYPE 12 24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT6A MUTATED      0    4
  KRT6A WILD-TYPE   12   24
                        clus
vv                       KRT6A MUTATED KRT6A WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             4              24
[1] 2 2
[1] FALSE

Clustering(73) Variable = CYP2F1 MUTATION ANALYSIS
D73V1, survival
                  sevent
clus2               0  1
  CYP2F1 MUTATED    3  1
  CYP2F1 WILD-TYPE 31  5
  CYP2F1 MUTATED CYP2F1 WILD-TYPE 
               4               36 
  CYP2F1 MUTATED CYP2F1 WILD-TYPE 
               1                5 
$`CYP2F1 MUTATED`
TCGA-FA-A86F TCGA-FF-8047 TCGA-G8-6324 TCGA-GR-7353 
       18.18         4.14        41.16        98.07 

$`CYP2F1 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
        8.15        14.04        35.54        31.10        31.73        24.69 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       31.96        51.98        42.71        43.86        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  CYP2F1 MUTATED CYP2F1 WILD-TYPE 
            4.14             0.03 
  CYP2F1 MUTATED CYP2F1 WILD-TYPE 
           98.07           128.12 
  CYP2F1 MUTATED CYP2F1 WILD-TYPE 
           29.67            25.53 
[1] "4.1 - 98.1 (29.7)"  "0.0 - 128.1 (25.5)"
[1] "hr=" "1.7"
D73V2, continuous
D73V3, binary
                  cls
clus                0  1
  CYP2F1 MUTATED    3  1
  CYP2F1 WILD-TYPE 21 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2F1 MUTATED      3    1
  CYP2F1 WILD-TYPE   21   15
        clus
vv       CYP2F1 MUTATED CYP2F1 WILD-TYPE
  FEMALE              3               21
  MALE                1               15
[1] 2 2
[1] FALSE
D73V4, binary
                  cls
clus                0  1
  CYP2F1 MUTATED    4  0
  CYP2F1 WILD-TYPE 29  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2F1 MUTATED      4    0
  CYP2F1 WILD-TYPE   29    6
     clus
vv    CYP2F1 MUTATED CYP2F1 WILD-TYPE
  NO               4               29
  YES              0                6
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  CYP2F1 MUTATED                                                                                   4
  CYP2F1 WILD-TYPE                                                                                29
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  CYP2F1 MUTATED                          0                                  0
  CYP2F1 WILD-TYPE                        3                                  4
D73V5, multiclass
                                                                                   clus
vv                                                                                  CYP2F1 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              4
  PRIMARY DLBCL OF THE CNS                                                                       0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             0
                                                                                   clus
vv                                                                                  CYP2F1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               29
  PRIMARY DLBCL OF THE CNS                                                                         3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CYP2F1 MUTATED       1                         1     2
  CYP2F1 WILD-TYPE    17                         0    19
D73V6, multiclass
                           clus
vv                          CYP2F1 MUTATED CYP2F1 WILD-TYPE
  ASIAN                                  1               17
  BLACK OR AFRICAN AMERICAN              1                0
  WHITE                                  2               19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                  cls
clus                0  1
  CYP2F1 MUTATED    0  4
  CYP2F1 WILD-TYPE 12 24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2F1 MUTATED      0    4
  CYP2F1 WILD-TYPE   12   24
                        clus
vv                       CYP2F1 MUTATED CYP2F1 WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              4               24
[1] 2 2
[1] FALSE

Clustering(74) Variable = FCGBP MUTATION ANALYSIS
D74V1, survival
                 sevent
clus2              0  1
  FCGBP MUTATED    3  2
  FCGBP WILD-TYPE 31  4
  FCGBP MUTATED FCGBP WILD-TYPE 
              5              35 
  FCGBP MUTATED FCGBP WILD-TYPE 
              2               4 
$`FCGBP MUTATED`
TCGA-FA-A4XK TCGA-FF-A7CW TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D5 
       23.28        26.01        41.16        98.07        42.71 

$`FCGBP WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         1.91        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CX 
        4.14        27.35        22.32         9.80        10.29        12.66 
TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT 
       31.96        51.98        43.86        57.17        32.28        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
      128.12        24.00        53.16        45.14       109.58        25.15 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
      111.58        12.85        25.91         0.03         0.56 

  FCGBP MUTATED FCGBP WILD-TYPE 
          23.28            0.03 
  FCGBP MUTATED FCGBP WILD-TYPE 
          98.07          128.12 
  FCGBP MUTATED FCGBP WILD-TYPE 
          41.16           24.69 
[1] "23.3 - 98.1 (41.2)" "0.0 - 128.1 (24.7)"
[1] "hr=" "2.3"
D74V2, continuous
D74V3, binary
                 cls
clus               0  1
  FCGBP MUTATED    2  3
  FCGBP WILD-TYPE 22 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      2    3
  FCGBP WILD-TYPE   22   13
        clus
vv       FCGBP MUTATED FCGBP WILD-TYPE
  FEMALE             2              22
  MALE               3              13
[1] 2 2
[1] FALSE
D74V4, binary
                 cls
clus               0  1
  FCGBP MUTATED    5  0
  FCGBP WILD-TYPE 28  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      5    0
  FCGBP WILD-TYPE   28    6
     clus
vv    FCGBP MUTATED FCGBP WILD-TYPE
  NO              5              28
  YES             0               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  FCGBP MUTATED                                                                                   5
  FCGBP WILD-TYPE                                                                                28
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  FCGBP MUTATED                          0                                  0
  FCGBP WILD-TYPE                        3                                  4
D74V5, multiclass
                                                                                   clus
vv                                                                                  FCGBP MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             5
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  FCGBP WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              28
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FCGBP MUTATED       2                         1     2
  FCGBP WILD-TYPE    16                         0    19
D74V6, multiclass
                           clus
vv                          FCGBP MUTATED FCGBP WILD-TYPE
  ASIAN                                 2              16
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 2              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                 cls
clus               0  1
  FCGBP MUTATED    0  5
  FCGBP WILD-TYPE 12 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCGBP MUTATED      0    5
  FCGBP WILD-TYPE   12   23
                        clus
vv                       FCGBP MUTATED FCGBP WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             5              23
[1] 2 2
[1] FALSE

Clustering(75) Variable = ZNF493 MUTATION ANALYSIS
D75V1, survival
                  sevent
clus2               0  1
  ZNF493 MUTATED    3  1
  ZNF493 WILD-TYPE 31  5
  ZNF493 MUTATED ZNF493 WILD-TYPE 
               4               36 
  ZNF493 MUTATED ZNF493 WILD-TYPE 
               1                5 
$`ZNF493 MUTATED`
TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D9 TCGA-GS-A9TT 
       41.16        98.07        57.17        38.24 

$`ZNF493 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       24.69         4.14        27.35        22.32         9.80        10.29 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
       26.01        12.66        31.96        51.98        42.71        43.86 
TCGA-GS-A9TQ TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       32.28       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  ZNF493 MUTATED ZNF493 WILD-TYPE 
           38.24             0.03 
  ZNF493 MUTATED ZNF493 WILD-TYPE 
           98.07           128.12 
  ZNF493 MUTATED ZNF493 WILD-TYPE 
          49.165           24.655 
[1] "38.2 - 98.1 (49.2)" "0.0 - 128.1 (24.7)"
[1] "hr=" "1.1"
D75V2, continuous
D75V3, binary
                  cls
clus                0  1
  ZNF493 MUTATED    2  2
  ZNF493 WILD-TYPE 22 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF493 MUTATED      2    2
  ZNF493 WILD-TYPE   22   14
        clus
vv       ZNF493 MUTATED ZNF493 WILD-TYPE
  FEMALE              2               22
  MALE                2               14
[1] 2 2
[1] FALSE
D75V4, binary
                  cls
clus                0  1
  ZNF493 MUTATED    3  1
  ZNF493 WILD-TYPE 30  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF493 MUTATED      3    1
  ZNF493 WILD-TYPE   30    5
     clus
vv    ZNF493 MUTATED ZNF493 WILD-TYPE
  NO               3               30
  YES              1                5
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  ZNF493 MUTATED                                                                                   4
  ZNF493 WILD-TYPE                                                                                29
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  ZNF493 MUTATED                          0                                  0
  ZNF493 WILD-TYPE                        3                                  4
D75V5, multiclass
                                                                                   clus
vv                                                                                  ZNF493 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              4
  PRIMARY DLBCL OF THE CNS                                                                       0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             0
                                                                                   clus
vv                                                                                  ZNF493 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               29
  PRIMARY DLBCL OF THE CNS                                                                         3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF493 MUTATED       0                         1     3
  ZNF493 WILD-TYPE    18                         0    18
D75V6, multiclass
                           clus
vv                          ZNF493 MUTATED ZNF493 WILD-TYPE
  ASIAN                                  0               18
  BLACK OR AFRICAN AMERICAN              1                0
  WHITE                                  3               18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                  cls
clus                0  1
  ZNF493 MUTATED    1  3
  ZNF493 WILD-TYPE 11 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF493 MUTATED      1    3
  ZNF493 WILD-TYPE   11   25
                        clus
vv                       ZNF493 MUTATED ZNF493 WILD-TYPE
  HISPANIC OR LATINO                  1               11
  NOT HISPANIC OR LATINO              3               25
[1] 2 2
[1] FALSE

Clustering(76) Variable = HLA-B MUTATION ANALYSIS
D76V1, survival
                 sevent
clus2              0  1
  HLA-B MUTATED    5  1
  HLA-B WILD-TYPE 29  5
  HLA-B MUTATED HLA-B WILD-TYPE 
              6              34 
  HLA-B MUTATED HLA-B WILD-TYPE 
              1               5 
$`HLA-B MUTATED`
TCGA-FA-8693 TCGA-FA-A7DS TCGA-FF-8041 TCGA-G8-6324 TCGA-GR-7353 TCGA-GS-A9TZ 
        4.34        23.64        35.54        41.16        98.07        25.15 

$`HLA-B WILD-TYPE`
TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34        23.28         1.91        24.62         8.15        14.04 
TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       18.18        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT 
       51.98        42.71        43.86        57.17        32.28        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9U3 
      128.12        24.00        53.16        45.14       109.58       111.58 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85        25.91         0.03         0.56 

  HLA-B MUTATED HLA-B WILD-TYPE 
           4.34            0.03 
  HLA-B MUTATED HLA-B WILD-TYPE 
          98.07          128.12 
  HLA-B MUTATED HLA-B WILD-TYPE 
         30.345          25.300 
[1] "4.3 - 98.1 (30.3)"  "0.0 - 128.1 (25.3)"
[1] "hr=" "1"  
D76V2, continuous
D76V3, binary
                 cls
clus               0  1
  HLA-B MUTATED    3  3
  HLA-B WILD-TYPE 21 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      3    3
  HLA-B WILD-TYPE   21   13
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  FEMALE             3              21
  MALE               3              13
[1] 2 2
[1] FALSE
D76V4, binary
                 cls
clus               0  1
  HLA-B MUTATED    5  1
  HLA-B WILD-TYPE 28  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      5    1
  HLA-B WILD-TYPE   28    5
     clus
vv    HLA-B MUTATED HLA-B WILD-TYPE
  NO              5              28
  YES             1               5
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  HLA-B MUTATED                                                                                   4
  HLA-B WILD-TYPE                                                                                29
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  HLA-B MUTATED                          0                                  2
  HLA-B WILD-TYPE                        3                                  2
D76V5, multiclass
                                                                                   clus
vv                                                                                  HLA-B MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             4
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            2
                                                                                   clus
vv                                                                                  HLA-B WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              29
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HLA-B MUTATED       2                         1     3
  HLA-B WILD-TYPE    16                         0    18
D76V6, multiclass
                           clus
vv                          HLA-B MUTATED HLA-B WILD-TYPE
  ASIAN                                 2              16
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 3              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                 cls
clus               0  1
  HLA-B MUTATED    1  5
  HLA-B WILD-TYPE 11 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      1    5
  HLA-B WILD-TYPE   11   23
                        clus
vv                       HLA-B MUTATED HLA-B WILD-TYPE
  HISPANIC OR LATINO                 1              11
  NOT HISPANIC OR LATINO             5              23
[1] 2 2
[1] FALSE

Clustering(77) Variable = FCRLA MUTATION ANALYSIS
D77V1, survival
                 sevent
clus2              0  1
  FCRLA MUTATED    2  1
  FCRLA WILD-TYPE 32  5
  FCRLA MUTATED FCRLA WILD-TYPE 
              3              37 
  FCRLA MUTATED FCRLA WILD-TYPE 
              1               5 
$`FCRLA MUTATED`
TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D9 
       41.16        98.07        57.17 

$`FCRLA WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       24.69         4.14        27.35        22.32         9.80        10.29 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
       26.01        12.66        31.96        51.98        42.71        43.86 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       32.28        38.24       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  FCRLA MUTATED FCRLA WILD-TYPE 
          41.16            0.03 
  FCRLA MUTATED FCRLA WILD-TYPE 
          98.07          128.12 
  FCRLA MUTATED FCRLA WILD-TYPE 
          57.17           24.69 
[1] "41.2 - 98.1 (57.2)" "0.0 - 128.1 (24.7)"
[1] "hr=" "1.4"
D77V2, continuous
D77V3, binary
                 cls
clus               0  1
  FCRLA MUTATED    2  1
  FCRLA WILD-TYPE 22 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRLA MUTATED      2    1
  FCRLA WILD-TYPE   22   15
        clus
vv       FCRLA MUTATED FCRLA WILD-TYPE
  FEMALE             2              22
  MALE               1              15
[1] 2 2
[1] FALSE
D77V4, binary
                 cls
clus               0  1
  FCRLA MUTATED    3  0
  FCRLA WILD-TYPE 30  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRLA MUTATED      3    0
  FCRLA WILD-TYPE   30    6
     clus
vv    FCRLA MUTATED FCRLA WILD-TYPE
  NO              3              30
  YES             0               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  FCRLA MUTATED                                                                                   3
  FCRLA WILD-TYPE                                                                                30
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  FCRLA MUTATED                          0                                  0
  FCRLA WILD-TYPE                        3                                  4
D77V5, multiclass
                                                                                   clus
vv                                                                                  FCRLA MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             3
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  FCRLA WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              30
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FCRLA MUTATED       0                         1     2
  FCRLA WILD-TYPE    18                         0    19
D77V6, multiclass
                           clus
vv                          FCRLA MUTATED FCRLA WILD-TYPE
  ASIAN                                 0              18
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 2              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                 cls
clus               0  1
  FCRLA MUTATED    0  3
  FCRLA WILD-TYPE 12 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRLA MUTATED      0    3
  FCRLA WILD-TYPE   12   25
                        clus
vv                       FCRLA MUTATED FCRLA WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             3              25
[1] 2 2
[1] FALSE

Clustering(78) Variable = KLRC2 MUTATION ANALYSIS
D78V1, survival
                 sevent
clus2              0  1
  KLRC2 MUTATED    5  0
  KLRC2 WILD-TYPE 29  6
  KLRC2 MUTATED KLRC2 WILD-TYPE 
              5              35 
  KLRC2 MUTATED KLRC2 WILD-TYPE 
              0               6 
$`KLRC2 MUTATED`
TCGA-FA-A4BB TCGA-FF-8062 TCGA-FM-8000 TCGA-GR-7353 TCGA-GR-A4D9 
        4.34        22.32        31.96        98.07        57.17 

$`KLRC2 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34        23.28         1.91        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
        4.14        27.35         9.80        10.29        26.01        12.66 
TCGA-G8-6324 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GS-A9TQ TCGA-GS-A9TT 
       41.16        51.98        42.71        43.86        32.28        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
      128.12        24.00        53.16        45.14       109.58        25.15 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
      111.58        12.85        25.91         0.03         0.56 

  KLRC2 MUTATED KLRC2 WILD-TYPE 
           4.34            0.03 
  KLRC2 MUTATED KLRC2 WILD-TYPE 
          98.07          128.12 
  KLRC2 MUTATED KLRC2 WILD-TYPE 
          31.96           25.15 
[1] "4.3 - 98.1 (32.0)"  "0.0 - 128.1 (25.1)"
[1] "hr="     "2.3e+08"
D78V2, continuous
D78V3, binary
                 cls
clus               0  1
  KLRC2 MUTATED    3  2
  KLRC2 WILD-TYPE 21 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRC2 MUTATED      3    2
  KLRC2 WILD-TYPE   21   14
        clus
vv       KLRC2 MUTATED KLRC2 WILD-TYPE
  FEMALE             3              21
  MALE               2              14
[1] 2 2
[1] FALSE
D78V4, binary
                 cls
clus               0  1
  KLRC2 MUTATED    5  0
  KLRC2 WILD-TYPE 28  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRC2 MUTATED      5    0
  KLRC2 WILD-TYPE   28    6
     clus
vv    KLRC2 MUTATED KLRC2 WILD-TYPE
  NO              5              28
  YES             0               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  KLRC2 MUTATED                                                                                   5
  KLRC2 WILD-TYPE                                                                                28
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  KLRC2 MUTATED                          0                                  0
  KLRC2 WILD-TYPE                        3                                  4
D78V5, multiclass
                                                                                   clus
vv                                                                                  KLRC2 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             5
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  KLRC2 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              28
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KLRC2 MUTATED       1                         0     4
  KLRC2 WILD-TYPE    17                         1    17
D78V6, multiclass
                           clus
vv                          KLRC2 MUTATED KLRC2 WILD-TYPE
  ASIAN                                 1              17
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 4              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                 cls
clus               0  1
  KLRC2 MUTATED    0  5
  KLRC2 WILD-TYPE 12 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRC2 MUTATED      0    5
  KLRC2 WILD-TYPE   12   23
                        clus
vv                       KLRC2 MUTATED KLRC2 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             5              23
[1] 2 2
[1] FALSE

Clustering(79) Variable = CD79B MUTATION ANALYSIS
D79V1, survival
                 sevent
clus2              0  1
  CD79B MUTATED    4  1
  CD79B WILD-TYPE 30  5
  CD79B MUTATED CD79B WILD-TYPE 
              5              35 
  CD79B MUTATED CD79B WILD-TYPE 
              1               5 
$`CD79B MUTATED`
TCGA-FA-A6HO TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-RQ-A68N TCGA-RQ-AAAT 
       24.62         9.80        10.29        25.91         0.56 

$`CD79B WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        23.28         1.91        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
        4.14        27.35        22.32        26.01        12.66        31.96 
TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       41.16        98.07        51.98        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       32.28        38.24       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85         0.03 

  CD79B MUTATED CD79B WILD-TYPE 
           0.56            0.03 
  CD79B MUTATED CD79B WILD-TYPE 
          25.91          128.12 
  CD79B MUTATED CD79B WILD-TYPE 
          10.29           27.35 
[1] "0.6 - 25.9 (10.3)"  "0.0 - 128.1 (27.4)"
[1] "hr=" "2.5"
D79V2, continuous
D79V3, binary
                 cls
clus               0  1
  CD79B MUTATED    2  3
  CD79B WILD-TYPE 22 13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79B MUTATED      2    3
  CD79B WILD-TYPE   22   13
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  FEMALE             2              22
  MALE               3              13
[1] 2 2
[1] FALSE
D79V4, binary
                 cls
clus               0  1
  CD79B MUTATED    5  0
  CD79B WILD-TYPE 28  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79B MUTATED      5    0
  CD79B WILD-TYPE   28    6
     clus
vv    CD79B MUTATED CD79B WILD-TYPE
  NO              5              28
  YES             0               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  CD79B MUTATED                                                                                   3
  CD79B WILD-TYPE                                                                                30
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  CD79B MUTATED                          2                                  0
  CD79B WILD-TYPE                        1                                  4
D79V5, multiclass
                                                                                   clus
vv                                                                                  CD79B MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             3
  PRIMARY DLBCL OF THE CNS                                                                      2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  CD79B WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              30
  PRIMARY DLBCL OF THE CNS                                                                        1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CD79B MUTATED       3                         0     2
  CD79B WILD-TYPE    15                         1    19
D79V6, multiclass
                           clus
vv                          CD79B MUTATED CD79B WILD-TYPE
  ASIAN                                 3              15
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 2              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                 cls
clus               0  1
  CD79B MUTATED    2  3
  CD79B WILD-TYPE 10 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79B MUTATED      2    3
  CD79B WILD-TYPE   10   25
                        clus
vv                       CD79B MUTATED CD79B WILD-TYPE
  HISPANIC OR LATINO                 2              10
  NOT HISPANIC OR LATINO             3              25
[1] 2 2
[1] FALSE

Clustering(80) Variable = TMSB4X MUTATION ANALYSIS
D80V1, survival
                  sevent
clus2               0  1
  TMSB4X MUTATED    4  1
  TMSB4X WILD-TYPE 30  5
  TMSB4X MUTATED TMSB4X WILD-TYPE 
               5               35 
  TMSB4X MUTATED TMSB4X WILD-TYPE 
               1                5 
$`TMSB4X MUTATED`
TCGA-FA-A6HN TCGA-FF-8042 TCGA-FF-8062 TCGA-GS-A9TV TCGA-GS-A9TW 
        1.91        31.10        22.32        24.00        53.16 

$`TMSB4X WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        23.28        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       14.04        18.18        35.54        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       27.35         9.80        10.29        26.01        12.66        31.96 
TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       41.16        98.07        51.98        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
       32.28        38.24       128.12        45.14       109.58        25.15 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
      111.58        12.85        25.91         0.03         0.56 

  TMSB4X MUTATED TMSB4X WILD-TYPE 
            1.91             0.03 
  TMSB4X MUTATED TMSB4X WILD-TYPE 
           53.16           128.12 
  TMSB4X MUTATED TMSB4X WILD-TYPE 
           24.00            25.91 
[1] "1.9 - 53.2 (24.0)"  "0.0 - 128.1 (25.9)"
[1] "hr=" "1.5"
D80V2, continuous
D80V3, binary
                  cls
clus                0  1
  TMSB4X MUTATED    4  1
  TMSB4X WILD-TYPE 20 15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMSB4X MUTATED      4    1
  TMSB4X WILD-TYPE   20   15
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  FEMALE              4               20
  MALE                1               15
[1] 2 2
[1] FALSE
D80V4, binary
                  cls
clus                0  1
  TMSB4X MUTATED    3  2
  TMSB4X WILD-TYPE 30  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMSB4X MUTATED      3    2
  TMSB4X WILD-TYPE   30    4
     clus
vv    TMSB4X MUTATED TMSB4X WILD-TYPE
  NO               3               30
  YES              2                4
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  TMSB4X MUTATED                                                                                   3
  TMSB4X WILD-TYPE                                                                                30
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  TMSB4X MUTATED                          0                                  2
  TMSB4X WILD-TYPE                        3                                  2
D80V5, multiclass
                                                                                   clus
vv                                                                                  TMSB4X MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              3
  PRIMARY DLBCL OF THE CNS                                                                       0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             2
                                                                                   clus
vv                                                                                  TMSB4X WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               30
  PRIMARY DLBCL OF THE CNS                                                                         3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TMSB4X MUTATED       3                         0     2
  TMSB4X WILD-TYPE    15                         1    19
D80V6, multiclass
                           clus
vv                          TMSB4X MUTATED TMSB4X WILD-TYPE
  ASIAN                                  3               15
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  2               19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, binary
                  cls
clus                0  1
  TMSB4X MUTATED    2  3
  TMSB4X WILD-TYPE 10 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMSB4X MUTATED      2    3
  TMSB4X WILD-TYPE   10   25
                        clus
vv                       TMSB4X MUTATED TMSB4X WILD-TYPE
  HISPANIC OR LATINO                  2               10
  NOT HISPANIC OR LATINO              3               25
[1] 2 2
[1] FALSE

Clustering(81) Variable = PRB1 MUTATION ANALYSIS
D81V1, survival
                sevent
clus2             0  1
  PRB1 MUTATED    3  2
  PRB1 WILD-TYPE 31  4
  PRB1 MUTATED PRB1 WILD-TYPE 
             5             35 
  PRB1 MUTATED PRB1 WILD-TYPE 
             2              4 
$`PRB1 MUTATED`
TCGA-FA-A6HN TCGA-G8-6324 TCGA-GR-7353 TCGA-GS-A9TW TCGA-GS-A9U3 
        1.91        41.16        98.07        53.16       111.58 

$`PRB1 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        23.28        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       12.66        31.96        51.98        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9TY 
       32.28        38.24       128.12        24.00        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15        12.85        25.91         0.03         0.56 

  PRB1 MUTATED PRB1 WILD-TYPE 
          1.91           0.03 
  PRB1 MUTATED PRB1 WILD-TYPE 
        111.58         128.12 
  PRB1 MUTATED PRB1 WILD-TYPE 
         53.16          24.69 
[1] "1.9 - 111.6 (53.2)" "0.0 - 128.1 (24.7)"
[1] "hr=" "2.6"
D81V2, continuous
D81V3, binary
                cls
clus              0  1
  PRB1 MUTATED    3  2
  PRB1 WILD-TYPE 21 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB1 MUTATED      3    2
  PRB1 WILD-TYPE   21   14
        clus
vv       PRB1 MUTATED PRB1 WILD-TYPE
  FEMALE            3             21
  MALE              2             14
[1] 2 2
[1] FALSE
D81V4, binary
                cls
clus              0  1
  PRB1 MUTATED    4  1
  PRB1 WILD-TYPE 29  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB1 MUTATED      4    1
  PRB1 WILD-TYPE   29    5
     clus
vv    PRB1 MUTATED PRB1 WILD-TYPE
  NO             4             29
  YES            1              5
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  PRB1 MUTATED                                                                                   4
  PRB1 WILD-TYPE                                                                                29
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  PRB1 MUTATED                          0                                  1
  PRB1 WILD-TYPE                        3                                  3
D81V5, multiclass
                                                                                   clus
vv                                                                                  PRB1 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)            4
  PRIMARY DLBCL OF THE CNS                                                                     0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                           1
                                                                                   clus
vv                                                                                  PRB1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             29
  PRIMARY DLBCL OF THE CNS                                                                       3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRB1 MUTATED       1                         1     3
  PRB1 WILD-TYPE    17                         0    18
D81V6, multiclass
                           clus
vv                          PRB1 MUTATED PRB1 WILD-TYPE
  ASIAN                                1             17
  BLACK OR AFRICAN AMERICAN            1              0
  WHITE                                3             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V7, binary
                cls
clus              0  1
  PRB1 MUTATED    2  3
  PRB1 WILD-TYPE 10 25
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB1 MUTATED      2    3
  PRB1 WILD-TYPE   10   25
                        clus
vv                       PRB1 MUTATED PRB1 WILD-TYPE
  HISPANIC OR LATINO                2             10
  NOT HISPANIC OR LATINO            3             25
[1] 2 2
[1] FALSE

Clustering(82) Variable = PCDHA7 MUTATION ANALYSIS
D82V1, survival
                  sevent
clus2               0  1
  PCDHA7 MUTATED    4  0
  PCDHA7 WILD-TYPE 30  6
  PCDHA7 MUTATED PCDHA7 WILD-TYPE 
               4               36 
  PCDHA7 MUTATED PCDHA7 WILD-TYPE 
               0                6 
$`PCDHA7 MUTATED`
TCGA-FA-8693 TCGA-FF-8042 TCGA-FF-8043 TCGA-RQ-A68N 
        4.34        31.10        31.73        25.91 

$`PCDHA7 WILD-TYPE`
TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34        23.28         1.91        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       14.04        18.18        35.54        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       41.16        98.07        51.98        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       32.28        38.24       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB TCGA-RQ-AAAT 
      109.58        25.15       111.58        12.85         0.03         0.56 

  PCDHA7 MUTATED PCDHA7 WILD-TYPE 
            4.34             0.03 
  PCDHA7 MUTATED PCDHA7 WILD-TYPE 
           31.73           128.12 
  PCDHA7 MUTATED PCDHA7 WILD-TYPE 
          28.505           24.920 
[1] "4.3 - 31.7 (28.5)"  "0.0 - 128.1 (24.9)"
[1] "hr="     "7.8e+07"
D82V2, continuous
D82V3, binary
                  cls
clus                0  1
  PCDHA7 MUTATED    2  2
  PCDHA7 WILD-TYPE 22 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDHA7 MUTATED      2    2
  PCDHA7 WILD-TYPE   22   14
        clus
vv       PCDHA7 MUTATED PCDHA7 WILD-TYPE
  FEMALE              2               22
  MALE                2               14
[1] 2 2
[1] FALSE
D82V4, binary
                  cls
clus                0  1
  PCDHA7 MUTATED    4  0
  PCDHA7 WILD-TYPE 29  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDHA7 MUTATED      4    0
  PCDHA7 WILD-TYPE   29    6
     clus
vv    PCDHA7 MUTATED PCDHA7 WILD-TYPE
  NO               4               29
  YES              0                6
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  PCDHA7 MUTATED                                                                                   3
  PCDHA7 WILD-TYPE                                                                                30
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  PCDHA7 MUTATED                          1                                  0
  PCDHA7 WILD-TYPE                        2                                  4
D82V5, multiclass
                                                                                   clus
vv                                                                                  PCDHA7 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              3
  PRIMARY DLBCL OF THE CNS                                                                       1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             0
                                                                                   clus
vv                                                                                  PCDHA7 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               30
  PRIMARY DLBCL OF THE CNS                                                                         2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PCDHA7 MUTATED       2                         0     2
  PCDHA7 WILD-TYPE    16                         1    19
D82V6, multiclass
                           clus
vv                          PCDHA7 MUTATED PCDHA7 WILD-TYPE
  ASIAN                                  2               16
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  2               19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V7, binary
                  cls
clus                0  1
  PCDHA7 MUTATED    1  3
  PCDHA7 WILD-TYPE 11 25
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDHA7 MUTATED      1    3
  PCDHA7 WILD-TYPE   11   25
                        clus
vv                       PCDHA7 MUTATED PCDHA7 WILD-TYPE
  HISPANIC OR LATINO                  1               11
  NOT HISPANIC OR LATINO              3               25
[1] 2 2
[1] FALSE

Clustering(83) Variable = OR5H14 MUTATION ANALYSIS
D83V1, survival
                  sevent
clus2               0  1
  OR5H14 MUTATED    2  1
  OR5H14 WILD-TYPE 32  5
  OR5H14 MUTATED OR5H14 WILD-TYPE 
               3               37 
  OR5H14 MUTATED OR5H14 WILD-TYPE 
               1                5 
$`OR5H14 MUTATED`
TCGA-FA-A7Q1 TCGA-FF-8042 TCGA-GS-A9TW 
        8.15        31.10        53.16 

$`OR5H14 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       14.04        18.18        35.54        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
       31.96        41.16        98.07        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TX 
       57.17        32.28        38.24       128.12        24.00        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  OR5H14 MUTATED OR5H14 WILD-TYPE 
            8.15             0.03 
  OR5H14 MUTATED OR5H14 WILD-TYPE 
           53.16           128.12 
  OR5H14 MUTATED OR5H14 WILD-TYPE 
           31.10            25.15 
[1] "8.2 - 53.2 (31.1)"  "0.0 - 128.1 (25.1)"
[1] "hr=" "2.4"
D83V2, continuous
D83V3, binary
                  cls
clus                0  1
  OR5H14 MUTATED    3  0
  OR5H14 WILD-TYPE 21 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5H14 MUTATED      3    0
  OR5H14 WILD-TYPE   21   16
        clus
vv       OR5H14 MUTATED OR5H14 WILD-TYPE
  FEMALE              3               21
  MALE                0               16
[1] 2 2
[1] FALSE
D83V4, binary
                  cls
clus                0  1
  OR5H14 MUTATED    2  1
  OR5H14 WILD-TYPE 31  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5H14 MUTATED      2    1
  OR5H14 WILD-TYPE   31    5
     clus
vv    OR5H14 MUTATED OR5H14 WILD-TYPE
  NO               2               31
  YES              1                5
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  OR5H14 MUTATED                                                                                   2
  OR5H14 WILD-TYPE                                                                                31
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  OR5H14 MUTATED                          0                                  1
  OR5H14 WILD-TYPE                        3                                  3
D83V5, multiclass
                                                                                   clus
vv                                                                                  OR5H14 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              2
  PRIMARY DLBCL OF THE CNS                                                                       0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             1
                                                                                   clus
vv                                                                                  OR5H14 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               31
  PRIMARY DLBCL OF THE CNS                                                                         3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OR5H14 MUTATED       2                         0     1
  OR5H14 WILD-TYPE    16                         1    20
D83V6, multiclass
                           clus
vv                          OR5H14 MUTATED OR5H14 WILD-TYPE
  ASIAN                                  2               16
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  1               20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V7, binary
                  cls
clus                0  1
  OR5H14 MUTATED    1  2
  OR5H14 WILD-TYPE 11 26
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5H14 MUTATED      1    2
  OR5H14 WILD-TYPE   11   26
                        clus
vv                       OR5H14 MUTATED OR5H14 WILD-TYPE
  HISPANIC OR LATINO                  1               11
  NOT HISPANIC OR LATINO              2               26
[1] 2 2
[1] FALSE

Clustering(84) Variable = PER3 MUTATION ANALYSIS
D84V1, survival
                sevent
clus2             0  1
  PER3 MUTATED    3  1
  PER3 WILD-TYPE 31  5
  PER3 MUTATED PER3 WILD-TYPE 
             4             36 
  PER3 MUTATED PER3 WILD-TYPE 
             1              5 
$`PER3 MUTATED`
TCGA-FF-A7CQ TCGA-G8-6324 TCGA-GR-A4D9 TCGA-GS-A9TW 
        9.80        41.16        57.17        53.16 

$`PER3 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CR TCGA-FF-A7CW 
       24.69         4.14        27.35        22.32        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
       12.66        31.96        98.07        51.98        42.71        43.86 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9TY 
       32.28        38.24       128.12        24.00        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  PER3 MUTATED PER3 WILD-TYPE 
          9.80           0.03 
  PER3 MUTATED PER3 WILD-TYPE 
         57.17         128.12 
  PER3 MUTATED PER3 WILD-TYPE 
         47.16          24.92 
[1] "9.8 - 57.2 (47.2)"  "0.0 - 128.1 (24.9)"
[1] "hr=" "1.3"
D84V2, continuous
D84V3, binary
                cls
clus              0  1
  PER3 MUTATED    3  1
  PER3 WILD-TYPE 21 15
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED      3    1
  PER3 WILD-TYPE   21   15
        clus
vv       PER3 MUTATED PER3 WILD-TYPE
  FEMALE            3             21
  MALE              1             15
[1] 2 2
[1] FALSE
D84V4, binary
                cls
clus              0  1
  PER3 MUTATED    3  1
  PER3 WILD-TYPE 30  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED      3    1
  PER3 WILD-TYPE   30    5
     clus
vv    PER3 MUTATED PER3 WILD-TYPE
  NO             3             30
  YES            1              5
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  PER3 MUTATED                                                                                   3
  PER3 WILD-TYPE                                                                                30
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  PER3 MUTATED                          0                                  1
  PER3 WILD-TYPE                        3                                  3
D84V5, multiclass
                                                                                   clus
vv                                                                                  PER3 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)            3
  PRIMARY DLBCL OF THE CNS                                                                     0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                           1
                                                                                   clus
vv                                                                                  PER3 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             30
  PRIMARY DLBCL OF THE CNS                                                                       3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PER3 MUTATED       1                         1     2
  PER3 WILD-TYPE    17                         0    19
D84V6, multiclass
                           clus
vv                          PER3 MUTATED PER3 WILD-TYPE
  ASIAN                                1             17
  BLACK OR AFRICAN AMERICAN            1              0
  WHITE                                2             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V7, binary
                cls
clus              0  1
  PER3 MUTATED    1  3
  PER3 WILD-TYPE 11 25
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED      1    3
  PER3 WILD-TYPE   11   25
                        clus
vv                       PER3 MUTATED PER3 WILD-TYPE
  HISPANIC OR LATINO                1             11
  NOT HISPANIC OR LATINO            3             25
[1] 2 2
[1] FALSE

Clustering(85) Variable = PABPC1 MUTATION ANALYSIS
D85V1, survival
                  sevent
clus2               0  1
  PABPC1 MUTATED    6  1
  PABPC1 WILD-TYPE 28  5
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               7               33 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               1                5 
$`PABPC1 MUTATED`
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-A7CW TCGA-G8-6324 
       35.54        31.10        24.69         4.14        26.01        41.16 
TCGA-RQ-AAAT 
        0.56 

$`PABPC1 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8043 TCGA-FF-8061 TCGA-FF-8062 
        8.15        14.04        18.18        31.73        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-7353 TCGA-GR-A4D4 
        9.80        10.29        12.66        31.96        98.07        51.98 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU 
       42.71        43.86        57.17        32.28        38.24       128.12 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 
       24.00        53.16        45.14       109.58        25.15       111.58 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
       12.85        25.91         0.03 

  PABPC1 MUTATED PABPC1 WILD-TYPE 
            0.56             0.03 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
           41.16           128.12 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
           26.01            25.15 
[1] "0.6 - 41.2 (26.0)"  "0.0 - 128.1 (25.1)"
[1] "hr=" "1.1"
D85V2, continuous
D85V3, binary
                  cls
clus                0  1
  PABPC1 MUTATED    5  2
  PABPC1 WILD-TYPE 19 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      5    2
  PABPC1 WILD-TYPE   19   14
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  FEMALE              5               19
  MALE                2               14
[1] 2 2
[1] FALSE
D85V4, binary
                  cls
clus                0  1
  PABPC1 MUTATED    7  0
  PABPC1 WILD-TYPE 26  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      7    0
  PABPC1 WILD-TYPE   26    6
     clus
vv    PABPC1 MUTATED PABPC1 WILD-TYPE
  NO               7               26
  YES              0                6
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  PABPC1 MUTATED                                                                                   5
  PABPC1 WILD-TYPE                                                                                28
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  PABPC1 MUTATED                          1                                  1
  PABPC1 WILD-TYPE                        2                                  3
D85V5, multiclass
                                                                                   clus
vv                                                                                  PABPC1 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              5
  PRIMARY DLBCL OF THE CNS                                                                       1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             1
                                                                                   clus
vv                                                                                  PABPC1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               28
  PRIMARY DLBCL OF THE CNS                                                                         2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PABPC1 MUTATED       5                         1     1
  PABPC1 WILD-TYPE    13                         0    20
D85V6, multiclass
                           clus
vv                          PABPC1 MUTATED PABPC1 WILD-TYPE
  ASIAN                                  5               13
  BLACK OR AFRICAN AMERICAN              1                0
  WHITE                                  1               20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V7, binary
                  cls
clus                0  1
  PABPC1 MUTATED    1  6
  PABPC1 WILD-TYPE 11 22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      1    6
  PABPC1 WILD-TYPE   11   22
                        clus
vv                       PABPC1 MUTATED PABPC1 WILD-TYPE
  HISPANIC OR LATINO                  1               11
  NOT HISPANIC OR LATINO              6               22
[1] 2 2
[1] FALSE

Clustering(86) Variable = ITGA6 MUTATION ANALYSIS
D86V1, survival
                 sevent
clus2              0  1
  ITGA6 MUTATED    2  1
  ITGA6 WILD-TYPE 32  5
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              3              37 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
              1               5 
$`ITGA6 MUTATED`
TCGA-FA-A7DS TCGA-G8-6324 TCGA-GR-7353 
       23.64        41.16        98.07 

$`ITGA6 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7Q1 
        4.34         4.34        23.28         1.91        24.62         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       12.66        31.96        51.98        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       32.28        38.24       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  ITGA6 MUTATED ITGA6 WILD-TYPE 
          23.64            0.03 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
          98.07          128.12 
  ITGA6 MUTATED ITGA6 WILD-TYPE 
          41.16           25.15 
[1] "23.6 - 98.1 (41.2)" "0.0 - 128.1 (25.1)"
[1] "hr=" "1.6"
D86V2, continuous
D86V3, binary
                 cls
clus               0  1
  ITGA6 MUTATED    2  1
  ITGA6 WILD-TYPE 22 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      2    1
  ITGA6 WILD-TYPE   22   15
        clus
vv       ITGA6 MUTATED ITGA6 WILD-TYPE
  FEMALE             2              22
  MALE               1              15
[1] 2 2
[1] FALSE
D86V4, binary
                 cls
clus               0  1
  ITGA6 MUTATED    3  0
  ITGA6 WILD-TYPE 30  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      3    0
  ITGA6 WILD-TYPE   30    6
     clus
vv    ITGA6 MUTATED ITGA6 WILD-TYPE
  NO              3              30
  YES             0               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  ITGA6 MUTATED                                                                                   3
  ITGA6 WILD-TYPE                                                                                30
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  ITGA6 MUTATED                          0                                  0
  ITGA6 WILD-TYPE                        3                                  4
D86V5, multiclass
                                                                                   clus
vv                                                                                  ITGA6 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             3
  PRIMARY DLBCL OF THE CNS                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  ITGA6 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              30
  PRIMARY DLBCL OF THE CNS                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ITGA6 MUTATED       1                         1     1
  ITGA6 WILD-TYPE    17                         0    20
D86V6, multiclass
                           clus
vv                          ITGA6 MUTATED ITGA6 WILD-TYPE
  ASIAN                                 1              17
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 1              20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V7, binary
                 cls
clus               0  1
  ITGA6 MUTATED    0  3
  ITGA6 WILD-TYPE 12 25
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA6 MUTATED      0    3
  ITGA6 WILD-TYPE   12   25
                        clus
vv                       ITGA6 MUTATED ITGA6 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             3              25
[1] 2 2
[1] FALSE

Clustering(87) Variable = IGSF3 MUTATION ANALYSIS
D87V1, survival
                 sevent
clus2              0  1
  IGSF3 MUTATED    5  1
  IGSF3 WILD-TYPE 29  5
  IGSF3 MUTATED IGSF3 WILD-TYPE 
              6              34 
  IGSF3 MUTATED IGSF3 WILD-TYPE 
              1               5 
$`IGSF3 MUTATED`
TCGA-FA-8693 TCGA-FA-A7Q1 TCGA-FF-8043 TCGA-GR-A4D5 TCGA-GS-A9TX TCGA-RQ-A6JB 
        4.34         8.15        31.73        42.71        45.14         0.03 

$`IGSF3 WILD-TYPE`
TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A82F 
        4.34        23.28         1.91        24.62        23.64        14.04 
TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       18.18        35.54        31.10        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       41.16        98.07        51.98        43.86        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TY TCGA-GS-A9TZ 
       38.24       128.12        24.00        53.16       109.58        25.15 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-AAAT 
      111.58        12.85        25.91         0.56 

  IGSF3 MUTATED IGSF3 WILD-TYPE 
           0.03            0.56 
  IGSF3 MUTATED IGSF3 WILD-TYPE 
          45.14          128.12 
  IGSF3 MUTATED IGSF3 WILD-TYPE 
          19.94           25.53 
[1] "0.0 - 45.1 (19.9)"  "0.6 - 128.1 (25.5)"
[1] "hr=" "1.4"
D87V2, continuous
D87V3, binary
                 cls
clus               0  1
  IGSF3 MUTATED    4  2
  IGSF3 WILD-TYPE 20 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF3 MUTATED      4    2
  IGSF3 WILD-TYPE   20   14
        clus
vv       IGSF3 MUTATED IGSF3 WILD-TYPE
  FEMALE             4              20
  MALE               2              14
[1] 2 2
[1] FALSE
D87V4, binary
                 cls
clus               0  1
  IGSF3 MUTATED    4  1
  IGSF3 WILD-TYPE 29  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF3 MUTATED      4    1
  IGSF3 WILD-TYPE   29    5
     clus
vv    IGSF3 MUTATED IGSF3 WILD-TYPE
  NO              4              29
  YES             1               5
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  IGSF3 MUTATED                                                                                   5
  IGSF3 WILD-TYPE                                                                                28
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  IGSF3 MUTATED                          1                                  0
  IGSF3 WILD-TYPE                        2                                  4
D87V5, multiclass
                                                                                   clus
vv                                                                                  IGSF3 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             5
  PRIMARY DLBCL OF THE CNS                                                                      1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  IGSF3 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              28
  PRIMARY DLBCL OF THE CNS                                                                        2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IGSF3 MUTATED       2                         0     4
  IGSF3 WILD-TYPE    16                         1    17
D87V6, multiclass
                           clus
vv                          IGSF3 MUTATED IGSF3 WILD-TYPE
  ASIAN                                 2              16
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 4              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V7, binary
                 cls
clus               0  1
  IGSF3 MUTATED    1  5
  IGSF3 WILD-TYPE 11 23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF3 MUTATED      1    5
  IGSF3 WILD-TYPE   11   23
                        clus
vv                       IGSF3 MUTATED IGSF3 WILD-TYPE
  HISPANIC OR LATINO                 1              11
  NOT HISPANIC OR LATINO             5              23
[1] 2 2
[1] FALSE

Clustering(88) Variable = KRTAP1-1 MUTATION ANALYSIS
D88V1, survival
                    sevent
clus2                 0  1
  KRTAP1-1 MUTATED    2  1
  KRTAP1-1 WILD-TYPE 32  5
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
                 3                 37 
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
                 1                  5 
$`KRTAP1-1 MUTATED`
TCGA-FF-8061 TCGA-G8-6324 TCGA-GR-7353 
       27.35        41.16        98.07 

$`KRTAP1-1 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
       24.69         4.14        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       12.66        31.96        51.98        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       32.28        38.24       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
             27.35               0.03 
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
             98.07             128.12 
  KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE 
             41.16              24.69 
[1] "27.4 - 98.1 (41.2)" "0.0 - 128.1 (24.7)"
[1] "hr=" "1.6"
D88V2, continuous
D88V3, binary
                    cls
clus                  0  1
  KRTAP1-1 MUTATED    1  2
  KRTAP1-1 WILD-TYPE 23 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP1-1 MUTATED      1    2
  KRTAP1-1 WILD-TYPE   23   14
        clus
vv       KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  FEMALE                1                 23
  MALE                  2                 14
[1] 2 2
[1] FALSE
D88V4, binary
                    cls
clus                  0  1
  KRTAP1-1 MUTATED    3  0
  KRTAP1-1 WILD-TYPE 30  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP1-1 MUTATED      3    0
  KRTAP1-1 WILD-TYPE   30    6
     clus
vv    KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  NO                 3                 30
  YES                0                  6
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  KRTAP1-1 MUTATED                                                                                   3
  KRTAP1-1 WILD-TYPE                                                                                30
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  KRTAP1-1 MUTATED                          0
  KRTAP1-1 WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  KRTAP1-1 MUTATED                                    0
  KRTAP1-1 WILD-TYPE                                  4
D88V5, multiclass
                                                                                   clus
vv                                                                                  KRTAP1-1 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                3
  PRIMARY DLBCL OF THE CNS                                                                         0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               0
                                                                                   clus
vv                                                                                  KRTAP1-1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 30
  PRIMARY DLBCL OF THE CNS                                                                           3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRTAP1-1 MUTATED       1                         1     1
  KRTAP1-1 WILD-TYPE    17                         0    20
D88V6, multiclass
                           clus
vv                          KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  ASIAN                                    1                 17
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                    1                 20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V7, binary
                    cls
clus                  0  1
  KRTAP1-1 MUTATED    0  3
  KRTAP1-1 WILD-TYPE 12 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP1-1 MUTATED      0    3
  KRTAP1-1 WILD-TYPE   12   25
                        clus
vv                       KRTAP1-1 MUTATED KRTAP1-1 WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                3                 25
[1] 2 2
[1] FALSE

Clustering(89) Variable = C15ORF39 MUTATION ANALYSIS
D89V1, survival
                    sevent
clus2                 0  1
  C15ORF39 MUTATED    2  1
  C15ORF39 WILD-TYPE 32  5
  C15ORF39 MUTATED C15ORF39 WILD-TYPE 
                 3                 37 
  C15ORF39 MUTATED C15ORF39 WILD-TYPE 
                 1                  5 
$`C15ORF39 MUTATED`
TCGA-G8-6324 TCGA-GR-7353 TCGA-RQ-A68N 
       41.16        98.07        25.91 

$`C15ORF39 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       24.69         4.14        27.35        22.32         9.80        10.29 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
       26.01        12.66        31.96        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       57.17        32.28        38.24       128.12        24.00        53.16 
TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB 
       45.14       109.58        25.15       111.58        12.85         0.03 
TCGA-RQ-AAAT 
        0.56 

  C15ORF39 MUTATED C15ORF39 WILD-TYPE 
             25.91               0.03 
  C15ORF39 MUTATED C15ORF39 WILD-TYPE 
             98.07             128.12 
  C15ORF39 MUTATED C15ORF39 WILD-TYPE 
             41.16              24.69 
[1] "25.9 - 98.1 (41.2)" "0.0 - 128.1 (24.7)"
[1] "hr=" "1.6"
D89V2, continuous
D89V3, binary
                    cls
clus                  0  1
  C15ORF39 MUTATED    1  2
  C15ORF39 WILD-TYPE 23 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF39 MUTATED      1    2
  C15ORF39 WILD-TYPE   23   14
        clus
vv       C15ORF39 MUTATED C15ORF39 WILD-TYPE
  FEMALE                1                 23
  MALE                  2                 14
[1] 2 2
[1] FALSE
D89V4, binary
                    cls
clus                  0  1
  C15ORF39 MUTATED    3  0
  C15ORF39 WILD-TYPE 30  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF39 MUTATED      3    0
  C15ORF39 WILD-TYPE   30    6
     clus
vv    C15ORF39 MUTATED C15ORF39 WILD-TYPE
  NO                 3                 30
  YES                0                  6
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  C15ORF39 MUTATED                                                                                   2
  C15ORF39 WILD-TYPE                                                                                31
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  C15ORF39 MUTATED                          1
  C15ORF39 WILD-TYPE                        2
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  C15ORF39 MUTATED                                    0
  C15ORF39 WILD-TYPE                                  4
D89V5, multiclass
                                                                                   clus
vv                                                                                  C15ORF39 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                2
  PRIMARY DLBCL OF THE CNS                                                                         1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               0
                                                                                   clus
vv                                                                                  C15ORF39 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 31
  PRIMARY DLBCL OF THE CNS                                                                           2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  C15ORF39 MUTATED       0                         1     2
  C15ORF39 WILD-TYPE    18                         0    19
D89V6, multiclass
                           clus
vv                          C15ORF39 MUTATED C15ORF39 WILD-TYPE
  ASIAN                                    0                 18
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                    2                 19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V7, binary
                    cls
clus                  0  1
  C15ORF39 MUTATED    1  2
  C15ORF39 WILD-TYPE 11 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF39 MUTATED      1    2
  C15ORF39 WILD-TYPE   11   26
                        clus
vv                       C15ORF39 MUTATED C15ORF39 WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO                2                 26
[1] 2 2
[1] FALSE

Clustering(90) Variable = ZNF880 MUTATION ANALYSIS
D90V1, survival
                  sevent
clus2               0  1
  ZNF880 MUTATED    6  2
  ZNF880 WILD-TYPE 28  4
  ZNF880 MUTATED ZNF880 WILD-TYPE 
               8               32 
  ZNF880 MUTATED ZNF880 WILD-TYPE 
               2                4 
$`ZNF880 MUTATED`
TCGA-FA-A6HN TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-G8-6324 
        1.91        18.18        35.54        31.73        24.69        41.16 
TCGA-GR-A4D4 TCGA-GS-A9TU 
       51.98       128.12 

$`ZNF880 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        23.28        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       14.04        31.10         4.14        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-7353 TCGA-GR-A4D5 
       10.29        26.01        12.66        31.96        98.07        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TV TCGA-GS-A9TW 
       43.86        57.17        32.28        38.24        24.00        53.16 
TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N 
       45.14       109.58        25.15       111.58        12.85        25.91 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  ZNF880 MUTATED ZNF880 WILD-TYPE 
            1.91             0.03 
  ZNF880 MUTATED ZNF880 WILD-TYPE 
          128.12           111.58 
  ZNF880 MUTATED ZNF880 WILD-TYPE 
          33.635           24.885 
[1] "1.9 - 128.1 (33.6)" "0.0 - 111.6 (24.9)"
[1] "hr=" "1.7"
D90V2, continuous
D90V3, binary
                  cls
clus                0  1
  ZNF880 MUTATED    5  3
  ZNF880 WILD-TYPE 19 13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF880 MUTATED      5    3
  ZNF880 WILD-TYPE   19   13
        clus
vv       ZNF880 MUTATED ZNF880 WILD-TYPE
  FEMALE              5               19
  MALE                3               13
[1] 2 2
[1] FALSE
D90V4, binary
                  cls
clus                0  1
  ZNF880 MUTATED    7  1
  ZNF880 WILD-TYPE 26  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF880 MUTATED      7    1
  ZNF880 WILD-TYPE   26    5
     clus
vv    ZNF880 MUTATED ZNF880 WILD-TYPE
  NO               7               26
  YES              1                5
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  ZNF880 MUTATED                                                                                   7
  ZNF880 WILD-TYPE                                                                                26
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  ZNF880 MUTATED                          0                                  1
  ZNF880 WILD-TYPE                        3                                  3
D90V5, multiclass
                                                                                   clus
vv                                                                                  ZNF880 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              7
  PRIMARY DLBCL OF THE CNS                                                                       0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             1
                                                                                   clus
vv                                                                                  ZNF880 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               26
  PRIMARY DLBCL OF THE CNS                                                                         3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF880 MUTATED       4                         1     3
  ZNF880 WILD-TYPE    14                         0    18
D90V6, multiclass
                           clus
vv                          ZNF880 MUTATED ZNF880 WILD-TYPE
  ASIAN                                  4               14
  BLACK OR AFRICAN AMERICAN              1                0
  WHITE                                  3               18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V7, binary
                  cls
clus                0  1
  ZNF880 MUTATED    1  7
  ZNF880 WILD-TYPE 11 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF880 MUTATED      1    7
  ZNF880 WILD-TYPE   11   21
                        clus
vv                       ZNF880 MUTATED ZNF880 WILD-TYPE
  HISPANIC OR LATINO                  1               11
  NOT HISPANIC OR LATINO              7               21
[1] 2 2
[1] FALSE

Clustering(91) Variable = NBPF15 MUTATION ANALYSIS
D91V1, survival
                  sevent
clus2               0  1
  NBPF15 MUTATED    4  0
  NBPF15 WILD-TYPE 30  6
  NBPF15 MUTATED NBPF15 WILD-TYPE 
               4               36 
  NBPF15 MUTATED NBPF15 WILD-TYPE 
               0                6 
$`NBPF15 MUTATED`
TCGA-FF-8042 TCGA-FF-8062 TCGA-FM-8000 TCGA-GR-A4D5 
       31.10        22.32        31.96        42.71 

$`NBPF15 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 
        8.15        14.04        18.18        35.54        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
        4.14        27.35         9.80        10.29        26.01        12.66 
TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       41.16        98.07        51.98        43.86        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  NBPF15 MUTATED NBPF15 WILD-TYPE 
           22.32             0.03 
  NBPF15 MUTATED NBPF15 WILD-TYPE 
           42.71           128.12 
  NBPF15 MUTATED NBPF15 WILD-TYPE 
           31.53            24.92 
[1] "22.3 - 42.7 (31.5)" "0.0 - 128.1 (24.9)"
[1] "hr="   "8e+07"
D91V2, continuous
D91V3, binary
                  cls
clus                0  1
  NBPF15 MUTATED    4  0
  NBPF15 WILD-TYPE 20 16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF15 MUTATED      4    0
  NBPF15 WILD-TYPE   20   16
        clus
vv       NBPF15 MUTATED NBPF15 WILD-TYPE
  FEMALE              4               20
  MALE                0               16
[1] 2 2
[1] FALSE
D91V4, binary
                  cls
clus                0  1
  NBPF15 MUTATED    4  0
  NBPF15 WILD-TYPE 29  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF15 MUTATED      4    0
  NBPF15 WILD-TYPE   29    6
     clus
vv    NBPF15 MUTATED NBPF15 WILD-TYPE
  NO               4               29
  YES              0                6
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  NBPF15 MUTATED                                                                                   4
  NBPF15 WILD-TYPE                                                                                29
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  NBPF15 MUTATED                          0                                  0
  NBPF15 WILD-TYPE                        3                                  4
D91V5, multiclass
                                                                                   clus
vv                                                                                  NBPF15 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              4
  PRIMARY DLBCL OF THE CNS                                                                       0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             0
                                                                                   clus
vv                                                                                  NBPF15 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               29
  PRIMARY DLBCL OF THE CNS                                                                         3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBPF15 MUTATED       2                         0     2
  NBPF15 WILD-TYPE    16                         1    19
D91V6, multiclass
                           clus
vv                          NBPF15 MUTATED NBPF15 WILD-TYPE
  ASIAN                                  2               16
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  2               19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V7, binary
                  cls
clus                0  1
  NBPF15 MUTATED    0  4
  NBPF15 WILD-TYPE 12 24
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF15 MUTATED      0    4
  NBPF15 WILD-TYPE   12   24
                        clus
vv                       NBPF15 MUTATED NBPF15 WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              4               24
[1] 2 2
[1] FALSE

Clustering(92) Variable = SLC22A16 MUTATION ANALYSIS
D92V1, survival
                    sevent
clus2                 0  1
  SLC22A16 MUTATED    2  1
  SLC22A16 WILD-TYPE 32  5
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                 3                 37 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                 1                  5 
$`SLC22A16 MUTATED`
TCGA-G8-6324 TCGA-GR-7353 TCGA-GR-A4D9 
       41.16        98.07        57.17 

$`SLC22A16 WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       24.69         4.14        27.35        22.32         9.80        10.29 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
       26.01        12.66        31.96        51.98        42.71        43.86 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       32.28        38.24       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
             41.16               0.03 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
             98.07             128.12 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
             57.17              24.69 
[1] "41.2 - 98.1 (57.2)" "0.0 - 128.1 (24.7)"
[1] "hr=" "1.4"
D92V2, continuous
D92V3, binary
                    cls
clus                  0  1
  SLC22A16 MUTATED    2  1
  SLC22A16 WILD-TYPE 22 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED      2    1
  SLC22A16 WILD-TYPE   22   15
        clus
vv       SLC22A16 MUTATED SLC22A16 WILD-TYPE
  FEMALE                2                 22
  MALE                  1                 15
[1] 2 2
[1] FALSE
D92V4, binary
                    cls
clus                  0  1
  SLC22A16 MUTATED    3  0
  SLC22A16 WILD-TYPE 30  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED      3    0
  SLC22A16 WILD-TYPE   30    6
     clus
vv    SLC22A16 MUTATED SLC22A16 WILD-TYPE
  NO                 3                 30
  YES                0                  6
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  SLC22A16 MUTATED                                                                                   3
  SLC22A16 WILD-TYPE                                                                                30
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  SLC22A16 MUTATED                          0
  SLC22A16 WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  SLC22A16 MUTATED                                    0
  SLC22A16 WILD-TYPE                                  4
D92V5, multiclass
                                                                                   clus
vv                                                                                  SLC22A16 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                3
  PRIMARY DLBCL OF THE CNS                                                                         0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               0
                                                                                   clus
vv                                                                                  SLC22A16 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 30
  PRIMARY DLBCL OF THE CNS                                                                           3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC22A16 MUTATED       0                         1     2
  SLC22A16 WILD-TYPE    18                         0    19
D92V6, multiclass
                           clus
vv                          SLC22A16 MUTATED SLC22A16 WILD-TYPE
  ASIAN                                    0                 18
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                    2                 19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V7, binary
                    cls
clus                  0  1
  SLC22A16 MUTATED    0  3
  SLC22A16 WILD-TYPE 12 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED      0    3
  SLC22A16 WILD-TYPE   12   25
                        clus
vv                       SLC22A16 MUTATED SLC22A16 WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                3                 25
[1] 2 2
[1] FALSE
