[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/22506396/DLBC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/22573828/transformed.cor.cli.txt"

nPatients in clinical file=48, in cluster file=48, common to both=48
[1] "Reduce the number of clustering variables from 37 to 36."
[1] 36 48
[1] "B2M MUTATION ANALYSIS"
[1] 3
  B2M MUTATED B2M WILD-TYPE 
           10            38 
  B2M MUTATED B2M WILD-TYPE 
           10            38 
[1] "MYD88 MUTATION ANALYSIS"
[1] 3
  MYD88 MUTATED MYD88 WILD-TYPE 
              3              45 
  MYD88 MUTATED MYD88 WILD-TYPE 
              3              45 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            14             34 
  MLL2 MUTATED MLL2 WILD-TYPE 
            14             34 
[1] "HLA-C MUTATION ANALYSIS"
[1] 3
  HLA-C MUTATED HLA-C WILD-TYPE 
              7              41 
  HLA-C MUTATED HLA-C WILD-TYPE 
              7              41 
[1] "ZNF814 MUTATION ANALYSIS"
[1] 3
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               7               41 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               7               41 
[1] "CD79B MUTATION ANALYSIS"
[1] 3
  CD79B MUTATED CD79B WILD-TYPE 
              5              43 
  CD79B MUTATED CD79B WILD-TYPE 
              5              43 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
             5             43 
  TP53 MUTATED TP53 WILD-TYPE 
             5             43 
[1] "TNFAIP3 MUTATION ANALYSIS"
[1] 3
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
                7                41 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
                7                41 
[1] "TMSB4X MUTATION ANALYSIS"
[1] 3
  TMSB4X MUTATED TMSB4X WILD-TYPE 
               6               42 
  TMSB4X MUTATED TMSB4X WILD-TYPE 
               6               42 
[1] "APLF MUTATION ANALYSIS"
[1] 3
  APLF MUTATED APLF WILD-TYPE 
             3             45 
  APLF MUTATED APLF WILD-TYPE 
             3             45 
[1] "RHPN2 MUTATION ANALYSIS"
[1] 3
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              7              41 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              7              41 
[1] "CIITA MUTATION ANALYSIS"
[1] 3
  CIITA MUTATED CIITA WILD-TYPE 
              5              43 
  CIITA MUTATED CIITA WILD-TYPE 
              5              43 
[1] "KDR MUTATION ANALYSIS"
[1] 3
  KDR MUTATED KDR WILD-TYPE 
            4            44 
  KDR MUTATED KDR WILD-TYPE 
            4            44 
[1] "CARD11 MUTATION ANALYSIS"
[1] 3
  CARD11 MUTATED CARD11 WILD-TYPE 
              10               38 
  CARD11 MUTATED CARD11 WILD-TYPE 
              10               38 
[1] "EZH2 MUTATION ANALYSIS"
[1] 3
  EZH2 MUTATED EZH2 WILD-TYPE 
             3             45 
  EZH2 MUTATED EZH2 WILD-TYPE 
             3             45 
[1] "NFKBIE MUTATION ANALYSIS"
[1] 3
  NFKBIE MUTATED NFKBIE WILD-TYPE 
               4               44 
  NFKBIE MUTATED NFKBIE WILD-TYPE 
               4               44 
[1] "MLH1 MUTATION ANALYSIS"
[1] 3
  MLH1 MUTATED MLH1 WILD-TYPE 
             3             45 
  MLH1 MUTATED MLH1 WILD-TYPE 
             3             45 
[1] "FAS MUTATION ANALYSIS"
[1] 3
  FAS MUTATED FAS WILD-TYPE 
            5            43 
  FAS MUTATED FAS WILD-TYPE 
            5            43 
[1] "ENOX1 MUTATION ANALYSIS"
[1] 3
  ENOX1 MUTATED ENOX1 WILD-TYPE 
              4              44 
  ENOX1 MUTATED ENOX1 WILD-TYPE 
              4              44 
[1] "SGK1 MUTATION ANALYSIS"
[1] 3
  SGK1 MUTATED SGK1 WILD-TYPE 
             4             44 
  SGK1 MUTATED SGK1 WILD-TYPE 
             4             44 
[1] "IFITM3 MUTATION ANALYSIS"
[1] 3
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               3               45 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               3               45 
[1] "APOB MUTATION ANALYSIS"
[1] 3
  APOB MUTATED APOB WILD-TYPE 
             3             45 
  APOB MUTATED APOB WILD-TYPE 
             3             45 
[1] "MCM8 MUTATION ANALYSIS"
[1] 3
  MCM8 MUTATED MCM8 WILD-TYPE 
             3             45 
  MCM8 MUTATED MCM8 WILD-TYPE 
             3             45 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               43 
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               43 
[1] "PCDHA10 MUTATION ANALYSIS"
[1] 3
  PCDHA10 MUTATED PCDHA10 WILD-TYPE 
                6                42 
  PCDHA10 MUTATED PCDHA10 WILD-TYPE 
                6                42 
[1] "LRRC16B MUTATION ANALYSIS"
[1] 3
  LRRC16B MUTATED LRRC16B WILD-TYPE 
                4                44 
  LRRC16B MUTATED LRRC16B WILD-TYPE 
                4                44 
[1] "PNPLA7 MUTATION ANALYSIS"
[1] 3
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
               3               45 
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
               3               45 
[1] "SLC16A8 MUTATION ANALYSIS"
[1] 3
  SLC16A8 MUTATED SLC16A8 WILD-TYPE 
                3                45 
  SLC16A8 MUTATED SLC16A8 WILD-TYPE 
                3                45 
[1] "PKHD1L1 MUTATION ANALYSIS"
[1] 3
  PKHD1L1 MUTATED PKHD1L1 WILD-TYPE 
                5                43 
  PKHD1L1 MUTATED PKHD1L1 WILD-TYPE 
                5                43 
[1] "HRCT1 MUTATION ANALYSIS"
[1] 3
  HRCT1 MUTATED HRCT1 WILD-TYPE 
              4              44 
  HRCT1 MUTATED HRCT1 WILD-TYPE 
              4              44 
[1] "TYRO3 MUTATION ANALYSIS"
[1] 3
  TYRO3 MUTATED TYRO3 WILD-TYPE 
              4              44 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
              4              44 
[1] "GSTZ1 MUTATION ANALYSIS"
[1] 3
  GSTZ1 MUTATED GSTZ1 WILD-TYPE 
              3              45 
  GSTZ1 MUTATED GSTZ1 WILD-TYPE 
              3              45 
[1] "STAT3 MUTATION ANALYSIS"
[1] 3
  STAT3 MUTATED STAT3 WILD-TYPE 
              7              41 
  STAT3 MUTATED STAT3 WILD-TYPE 
              7              41 
[1] "IRF8 MUTATION ANALYSIS"
[1] 3
  IRF8 MUTATED IRF8 WILD-TYPE 
             5             43 
  IRF8 MUTATED IRF8 WILD-TYPE 
             5             43 
[1] "TMEM30A MUTATION ANALYSIS"
[1] 3
  TMEM30A MUTATED TMEM30A WILD-TYPE 
                4                44 
  TMEM30A MUTATED TMEM30A WILD-TYPE 
                4                44 
[1] "UBE2A MUTATION ANALYSIS"
[1] 3
  UBE2A MUTATED UBE2A WILD-TYPE 
              4              44 
  UBE2A MUTATED UBE2A WILD-TYPE 
              4              44 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "NUMBER_OF_LYMPH_NODES"               
[15] "RACE"                                
[16] "ETHNICITY"                           

Input Data has 16 rows and 48 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=9,	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=37,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'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 7:'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 8:'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 9:'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 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NUMBER_OF_LYMPH_NODES is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'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 48 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"    "TUMOR_TISSUE_SITE" "GENDER"           
[4] "RADIATION_THERAPY" "HISTOLOGICAL_TYPE" "RACE"             
[7] "ETHNICITY"        
YEARS_TO_BIRTH, nv=34, binary=FALSE, numeric=TRUE
TUMOR_TISSUE_SITE, nv=13, binary=FALSE, numeric=FALSE
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 = B2M MUTATION ANALYSIS
D1V1, survival
               sevent
clus2            0  1
  B2M MUTATED    9  1
  B2M WILD-TYPE 29  8
  B2M MUTATED B2M WILD-TYPE 
           10            37 
  B2M MUTATED B2M WILD-TYPE 
            1             8 
$`B2M MUTATED`
TCGA-FF-8041 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6907 TCGA-GR-7351 
       35.54        27.35        22.32        31.96        19.56       150.51 
TCGA-GR-A4D9 TCGA-GS-A9TV TCGA-GS-A9TW TCGA-RQ-A6JB 
       57.17        24.00        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-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7353 
       51.98        70.06       211.23       116.81       196.60        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU 
       51.98        42.71        43.86        32.28        38.24       128.12 
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 

  B2M MUTATED B2M WILD-TYPE 
         0.03          0.56 
  B2M MUTATED B2M WILD-TYPE 
       150.51        211.23 
  B2M MUTATED B2M WILD-TYPE 
       29.655        26.010 
[1] "0.0 - 150.5 (29.7)" "0.6 - 211.2 (26.0)"
[1] "hr=" "2"  
D1V2, continuous
               vv
clus            ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  B2M MUTATED         0                  0    1     0      0     1     0
  B2M WILD-TYPE       2                  2    3     3      1     1     1
               vv
clus            OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  B2M MUTATED                       0             0               1
  B2M WILD-TYPE                     1             1               2
               vv
clus            SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  B2M MUTATED                                               1       0       2
  B2M WILD-TYPE                                             0       2       0
D1V3, multiclass
                                               clus
vv                                              B2M MUTATED B2M WILD-TYPE
  ADRENAL                                                 0             2
  ASCITES/PERITONEUM                                      0             2
  BONE                                                    1             3
  BRAIN                                                   0             3
  BREAST                                                  0             1
  COLON                                                   1             1
  LIVER                                                   0             1
  OTHER EXTRANODAL SITE                                   0             1
  PAROTID GLAND                                           0             1
  SMALL INTESTINE                                         1             2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)           1             0
  STOMACH                                                 0             2
  THYROID                                                 2             0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
               cls
clus             0  1
  B2M MUTATED    9  1
  B2M WILD-TYPE 17 21
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      9    1
  B2M WILD-TYPE   17   21
        clus
vv       B2M MUTATED B2M WILD-TYPE
  FEMALE           9            17
  MALE             1            21
[1] 2 2
[1] FALSE
D1V5, binary
               cls
clus             0  1
  B2M MUTATED    6  3
  B2M WILD-TYPE 34  4
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      6    3
  B2M WILD-TYPE   34    4
     clus
vv    B2M MUTATED B2M WILD-TYPE
  NO            6            34
  YES           3             4
[1] 2 2
[1] FALSE
               vv
clus            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  B2M MUTATED                                                                                   6
  B2M WILD-TYPE                                                                                35
               vv
clus            PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  B2M MUTATED                          1                                  3
  B2M WILD-TYPE                        2                                  1
D1V6, multiclass
                                                                                   clus
vv                                                                                  B2M 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                                                          3
                                                                                   clus
vv                                                                                  B2M WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)            35
  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     7
  B2M WILD-TYPE    15                         1    22
D1V7, multiclass
                           clus
vv                          B2M MUTATED B2M WILD-TYPE
  ASIAN                               3            15
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                               7            22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
               cls
clus             0  1
  B2M MUTATED    2  8
  B2M WILD-TYPE 10 28
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      2    8
  B2M WILD-TYPE   10   28
                        clus
vv                       B2M MUTATED B2M WILD-TYPE
  HISPANIC OR LATINO               2            10
  NOT HISPANIC OR LATINO           8            28
[1] 2 2
[1] FALSE

Clustering(2) Variable = MYD88 MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2              0  1
  MYD88 MUTATED    2  1
  MYD88 WILD-TYPE 36  8
  MYD88 MUTATED MYD88 WILD-TYPE 
              3              44 
  MYD88 MUTATED MYD88 WILD-TYPE 
              1               8 
$`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-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       31.96        41.16        51.98        70.06       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
      116.81       196.60       150.51        98.07        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-AAAT 
       25.91         0.56 

  MYD88 MUTATED MYD88 WILD-TYPE 
           0.03            0.56 
  MYD88 MUTATED MYD88 WILD-TYPE 
          12.66          211.23 
  MYD88 MUTATED MYD88 WILD-TYPE 
         10.290          31.415 
[1] "0.0 - 12.7 (10.3)"  "0.6 - 211.2 (31.4)"
[1] "hr=" "9.9"
D2V2, continuous
                 vv
clus              ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  MYD88 MUTATED         1                  0    1     1      0     0     0
  MYD88 WILD-TYPE       1                  2    3     2      1     2     1
                 vv
clus              OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  MYD88 MUTATED                       0             0               0
  MYD88 WILD-TYPE                     1             1               3
                 vv
clus              SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  MYD88 MUTATED                                               0       0       0
  MYD88 WILD-TYPE                                             1       2       2
D2V3, multiclass
                                               clus
vv                                              MYD88 MUTATED MYD88 WILD-TYPE
  ADRENAL                                                   1               1
  ASCITES/PERITONEUM                                        0               2
  BONE                                                      1               3
  BRAIN                                                     1               2
  BREAST                                                    0               1
  COLON                                                     0               2
  LIVER                                                     0               1
  OTHER EXTRANODAL SITE                                     0               1
  PAROTID GLAND                                             0               1
  SMALL INTESTINE                                           0               3
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)             0               1
  STOMACH                                                   0               2
  THYROID                                                   0               2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
                 cls
clus               0  1
  MYD88 MUTATED    1  2
  MYD88 WILD-TYPE 25 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYD88 MUTATED      1    2
  MYD88 WILD-TYPE   25   20
        clus
vv       MYD88 MUTATED MYD88 WILD-TYPE
  FEMALE             1              25
  MALE               2              20
[1] 2 2
[1] FALSE
D2V5, binary
                 cls
clus               0  1
  MYD88 MUTATED    2  0
  MYD88 WILD-TYPE 38  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYD88 MUTATED      2    0
  MYD88 WILD-TYPE   38    7
     clus
vv    MYD88 MUTATED MYD88 WILD-TYPE
  NO              2              38
  YES             0               7
[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                                                                                39
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  MYD88 MUTATED                          1                                  0
  MYD88 WILD-TYPE                        2                                  4
D2V6, 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)              39
  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    28
D2V7, multiclass
                           clus
vv                          MYD88 MUTATED MYD88 WILD-TYPE
  ASIAN                                 2              16
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 1              28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                 cls
clus               0  1
  MYD88 MUTATED    0  3
  MYD88 WILD-TYPE 12 33
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYD88 MUTATED      0    3
  MYD88 WILD-TYPE   12   33
                        clus
vv                       MYD88 MUTATED MYD88 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             3              33
[1] 2 2
[1] FALSE

Clustering(3) Variable = MLL2 MUTATION ANALYSIS
D3V1, survival
                sevent
clus2             0  1
  MLL2 MUTATED   12  2
  MLL2 WILD-TYPE 26  7
  MLL2 MUTATED MLL2 WILD-TYPE 
            14             33 
  MLL2 MUTATED MLL2 WILD-TYPE 
             2              7 
$`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-G8-6906 TCGA-G8-6914 
        4.14        10.29        26.01        31.96       211.23       196.60 
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-G8-6324 
       24.69        27.35        22.32         9.80        12.66        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-7353 
       51.98        70.06        19.56       116.81       150.51        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU 
       51.98        42.71        43.86        57.17        38.24       128.12 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 
       24.00        53.16        45.14        25.15       111.58        12.85 
TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.91         0.03         0.56 

  MLL2 MUTATED MLL2 WILD-TYPE 
          4.14           0.03 
  MLL2 MUTATED MLL2 WILD-TYPE 
        211.23         150.51 
  MLL2 MUTATED MLL2 WILD-TYPE 
        28.555         27.350 
[1] "4.1 - 211.2 (28.6)" "0.0 - 150.5 (27.4)"
[1] "hr=" "2.9"
D3V2, continuous
                vv
clus             ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  MLL2 MUTATED         0                  0    0     1      1     2     1
  MLL2 WILD-TYPE       2                  2    4     2      0     0     0
                vv
clus             OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  MLL2 MUTATED                       1             1               1
  MLL2 WILD-TYPE                     0             0               2
                vv
clus             SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  MLL2 MUTATED                                               0       0       0
  MLL2 WILD-TYPE                                             1       2       2
D3V3, multiclass
                                               clus
vv                                              MLL2 MUTATED MLL2 WILD-TYPE
  ADRENAL                                                  0              2
  ASCITES/PERITONEUM                                       0              2
  BONE                                                     0              4
  BRAIN                                                    1              2
  BREAST                                                   1              0
  COLON                                                    2              0
  LIVER                                                    1              0
  OTHER EXTRANODAL SITE                                    1              0
  PAROTID GLAND                                            1              0
  SMALL INTESTINE                                          1              2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)            0              1
  STOMACH                                                  0              2
  THYROID                                                  0              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
                cls
clus              0  1
  MLL2 MUTATED    9  5
  MLL2 WILD-TYPE 17 17
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      9    5
  MLL2 WILD-TYPE   17   17
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  FEMALE            9             17
  MALE              5             17
[1] 2 2
[1] FALSE
D3V5, binary
                cls
clus              0  1
  MLL2 MUTATED   14  0
  MLL2 WILD-TYPE 26  7
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     14    0
  MLL2 WILD-TYPE   26    7
     clus
vv    MLL2 MUTATED MLL2 WILD-TYPE
  NO            14             26
  YES            0              7
[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                                                                                27
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  MLL2 MUTATED                          0                                  0
  MLL2 WILD-TYPE                        3                                  4
D3V6, 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)             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
  MLL2 MUTATED       7                         0     7
  MLL2 WILD-TYPE    11                         1    22
D3V7, multiclass
                           clus
vv                          MLL2 MUTATED MLL2 WILD-TYPE
  ASIAN                                7             11
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                7             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
                cls
clus              0  1
  MLL2 MUTATED    2 12
  MLL2 WILD-TYPE 10 24
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      2   12
  MLL2 WILD-TYPE   10   24
                        clus
vv                       MLL2 MUTATED MLL2 WILD-TYPE
  HISPANIC OR LATINO                2             10
  NOT HISPANIC OR LATINO           12             24
[1] 2 2
[1] FALSE

Clustering(4) Variable = HLA-C MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2              0  1
  HLA-C MUTATED    3  4
  HLA-C WILD-TYPE 35  5
  HLA-C MUTATED HLA-C WILD-TYPE 
              7              40 
  HLA-C MUTATED HLA-C WILD-TYPE 
              4               5 
$`HLA-C MUTATED`
TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A7DS TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6906 
        4.34         1.91        23.64        41.16        51.98       211.23 
TCGA-G8-6909 
      116.81 

$`HLA-C WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F 
        4.34        23.28        24.62         8.15        14.04        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-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-G8-6326 TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 
       70.06        19.56       196.60       150.51        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 

  HLA-C MUTATED HLA-C WILD-TYPE 
           1.91            0.03 
  HLA-C MUTATED HLA-C WILD-TYPE 
         211.23          196.60 
  HLA-C MUTATED HLA-C WILD-TYPE 
          41.16           26.68 
[1] "1.9 - 211.2 (41.2)" "0.0 - 196.6 (26.7)"
[1] "hr=" "2.8"
D4V2, continuous
                 vv
clus              ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  HLA-C MUTATED         0                  1    0     0      1     0     1
  HLA-C WILD-TYPE       2                  1    4     3      0     2     0
                 vv
clus              OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  HLA-C MUTATED                       1             0               0
  HLA-C WILD-TYPE                     0             1               3
                 vv
clus              SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  HLA-C MUTATED                                               0       0       0
  HLA-C WILD-TYPE                                             1       2       2
D4V3, multiclass
                                               clus
vv                                              HLA-C MUTATED HLA-C WILD-TYPE
  ADRENAL                                                   0               2
  ASCITES/PERITONEUM                                        1               1
  BONE                                                      0               4
  BRAIN                                                     0               3
  BREAST                                                    1               0
  COLON                                                     0               2
  LIVER                                                     1               0
  OTHER EXTRANODAL SITE                                     1               0
  PAROTID GLAND                                             0               1
  SMALL INTESTINE                                           0               3
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)             0               1
  STOMACH                                                   0               2
  THYROID                                                   0               2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
                 cls
clus               0  1
  HLA-C MUTATED    2  5
  HLA-C WILD-TYPE 24 17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-C MUTATED      2    5
  HLA-C WILD-TYPE   24   17
        clus
vv       HLA-C MUTATED HLA-C WILD-TYPE
  FEMALE             2              24
  MALE               5              17
[1] 2 2
[1] FALSE
D4V5, binary
                 cls
clus               0  1
  HLA-C MUTATED    7  0
  HLA-C WILD-TYPE 33  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-C MUTATED      7    0
  HLA-C WILD-TYPE   33    7
     clus
vv    HLA-C MUTATED HLA-C WILD-TYPE
  NO              7              33
  YES             0               7
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  HLA-C MUTATED                                                                                   7
  HLA-C WILD-TYPE                                                                                34
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  HLA-C MUTATED                          0                                  0
  HLA-C WILD-TYPE                        3                                  4
D4V6, multiclass
                                                                                   clus
vv                                                                                  HLA-C 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                                                                                  HLA-C WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              34
  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
  HLA-C MUTATED       2                         1     4
  HLA-C WILD-TYPE    16                         0    25
D4V7, multiclass
                           clus
vv                          HLA-C MUTATED HLA-C WILD-TYPE
  ASIAN                                 2              16
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 4              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
                 cls
clus               0  1
  HLA-C MUTATED    0  7
  HLA-C WILD-TYPE 12 29
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-C MUTATED      0    7
  HLA-C WILD-TYPE   12   29
                        clus
vv                       HLA-C MUTATED HLA-C WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             7              29
[1] 2 2
[1] FALSE

Clustering(5) Variable = ZNF814 MUTATION ANALYSIS
D5V1, survival
                  sevent
clus2               0  1
  ZNF814 MUTATED    6  1
  ZNF814 WILD-TYPE 32  8
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               7               40 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               1                8 
$`ZNF814 MUTATED`
TCGA-FA-A7DS TCGA-FF-A7CQ TCGA-G8-6324 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TW 
       23.64         9.80        41.16        38.24       128.12        53.16 
TCGA-GS-A9U3 
      111.58 

$`ZNF814 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-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
        4.14        27.35        22.32        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       31.96        51.98        70.06       211.23        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        98.07        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
       57.17        32.28        24.00        45.14       109.58        25.15 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85        25.91         0.03         0.56 

  ZNF814 MUTATED ZNF814 WILD-TYPE 
            9.80             0.03 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
          128.12           211.23 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
           41.16            25.96 
[1] "9.8 - 128.1 (41.2)" "0.0 - 211.2 (26.0)"
[1] "hr=" "1.5"
D5V2, continuous
                  vv
clus               ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  ZNF814 MUTATED         1                  1    1     0      1     0     0
  ZNF814 WILD-TYPE       1                  1    3     3      0     2     1
                  vv
clus               OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  ZNF814 MUTATED                       0             0               0
  ZNF814 WILD-TYPE                     1             1               3
                  vv
clus               SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  ZNF814 MUTATED                                               0       0
  ZNF814 WILD-TYPE                                             1       2
                  vv
clus               THYROID
  ZNF814 MUTATED         0
  ZNF814 WILD-TYPE       2
D5V3, multiclass
                                               clus
vv                                              ZNF814 MUTATED ZNF814 WILD-TYPE
  ADRENAL                                                    1                1
  ASCITES/PERITONEUM                                         1                1
  BONE                                                       1                3
  BRAIN                                                      0                3
  BREAST                                                     1                0
  COLON                                                      0                2
  LIVER                                                      0                1
  OTHER EXTRANODAL SITE                                      0                1
  PAROTID GLAND                                              0                1
  SMALL INTESTINE                                            0                3
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)              0                1
  STOMACH                                                    0                2
  THYROID                                                    0                2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
                  cls
clus                0  1
  ZNF814 MUTATED    4  3
  ZNF814 WILD-TYPE 22 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      4    3
  ZNF814 WILD-TYPE   22   19
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  FEMALE              4               22
  MALE                3               19
[1] 2 2
[1] FALSE
D5V5, binary
                  cls
clus                0  1
  ZNF814 MUTATED    4  3
  ZNF814 WILD-TYPE 36  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      4    3
  ZNF814 WILD-TYPE   36    4
     clus
vv    ZNF814 MUTATED ZNF814 WILD-TYPE
  NO               4               36
  YES              3                4
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  ZNF814 MUTATED                                                                                   6
  ZNF814 WILD-TYPE                                                                                35
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  ZNF814 MUTATED                          0                                  1
  ZNF814 WILD-TYPE                        3                                  3
D5V6, multiclass
                                                                                   clus
vv                                                                                  ZNF814 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                                                                                  ZNF814 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               35
  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
  ZNF814 MUTATED       2                         1     4
  ZNF814 WILD-TYPE    16                         0    25
D5V7, multiclass
                           clus
vv                          ZNF814 MUTATED ZNF814 WILD-TYPE
  ASIAN                                  2               16
  BLACK OR AFRICAN AMERICAN              1                0
  WHITE                                  4               25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                  cls
clus                0  1
  ZNF814 MUTATED    4  3
  ZNF814 WILD-TYPE  8 33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      4    3
  ZNF814 WILD-TYPE    8   33
                        clus
vv                       ZNF814 MUTATED ZNF814 WILD-TYPE
  HISPANIC OR LATINO                  4                8
  NOT HISPANIC OR LATINO              3               33
[1] 2 2
[1] FALSE

Clustering(6) Variable = CD79B MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2              0  1
  CD79B MUTATED    4  1
  CD79B WILD-TYPE 34  8
  CD79B MUTATED CD79B WILD-TYPE 
              5              42 
  CD79B MUTATED CD79B WILD-TYPE 
              1               8 
$`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-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        70.06       211.23        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        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-A6JB 
       45.14       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          211.23 
  CD79B MUTATED CD79B WILD-TYPE 
         10.290          31.845 
[1] "0.6 - 25.9 (10.3)"  "0.0 - 211.2 (31.8)"
[1] "hr=" "2.5"
D6V2, continuous
                 vv
clus              ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  CD79B MUTATED         1                  0    0     3      0     0     0
  CD79B WILD-TYPE       1                  2    4     0      1     2     1
                 vv
clus              OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  CD79B MUTATED                       0             0               0
  CD79B WILD-TYPE                     1             1               3
                 vv
clus              SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  CD79B MUTATED                                               0       0       0
  CD79B WILD-TYPE                                             1       2       2
D6V3, multiclass
                                               clus
vv                                              CD79B MUTATED CD79B WILD-TYPE
  ADRENAL                                                   1               1
  ASCITES/PERITONEUM                                        0               2
  BONE                                                      0               4
  BRAIN                                                     3               0
  BREAST                                                    0               1
  COLON                                                     0               2
  LIVER                                                     0               1
  OTHER EXTRANODAL SITE                                     0               1
  PAROTID GLAND                                             0               1
  SMALL INTESTINE                                           0               3
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)             0               1
  STOMACH                                                   0               2
  THYROID                                                   0               2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
                 cls
clus               0  1
  CD79B MUTATED    2  3
  CD79B WILD-TYPE 24 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79B MUTATED      2    3
  CD79B WILD-TYPE   24   19
        clus
vv       CD79B MUTATED CD79B WILD-TYPE
  FEMALE             2              24
  MALE               3              19
[1] 2 2
[1] FALSE
D6V5, binary
                 cls
clus               0  1
  CD79B MUTATED    5  0
  CD79B WILD-TYPE 35  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79B MUTATED      5    0
  CD79B WILD-TYPE   35    7
     clus
vv    CD79B MUTATED CD79B WILD-TYPE
  NO              5              35
  YES             0               7
[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                                                                                38
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  CD79B MUTATED                          2                                  0
  CD79B WILD-TYPE                        1                                  4
D6V6, 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)              38
  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    27
D6V7, multiclass
                           clus
vv                          CD79B MUTATED CD79B WILD-TYPE
  ASIAN                                 3              15
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 2              27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
                 cls
clus               0  1
  CD79B MUTATED    2  3
  CD79B WILD-TYPE 10 33
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79B MUTATED      2    3
  CD79B WILD-TYPE   10   33
                        clus
vv                       CD79B MUTATED CD79B WILD-TYPE
  HISPANIC OR LATINO                 2              10
  NOT HISPANIC OR LATINO             3              33
[1] 2 2
[1] FALSE

Clustering(7) Variable = TP53 MUTATION ANALYSIS
D7V1, survival
                sevent
clus2             0  1
  TP53 MUTATED    5  0
  TP53 WILD-TYPE 33  9
  TP53 MUTATED TP53 WILD-TYPE 
             5             42 
  TP53 MUTATED TP53 WILD-TYPE 
             0              9 
$`TP53 MUTATED`
TCGA-FA-A82F TCGA-FF-8043 TCGA-GR-A4D4 TCGA-GS-A9TY TCGA-RQ-AAAT 
       14.04        31.73        51.98       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-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       31.96        41.16        51.98        70.06       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 
      116.81       196.60       150.51        98.07        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-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
       45.14        25.15       111.58        12.85        25.91         0.03 

  TP53 MUTATED TP53 WILD-TYPE 
          0.56           0.03 
  TP53 MUTATED TP53 WILD-TYPE 
        109.58         211.23 
  TP53 MUTATED TP53 WILD-TYPE 
         31.73          26.68 
[1] "0.6 - 109.6 (31.7)" "0.0 - 211.2 (26.7)"
[1] "hr="     "7.8e+07"
D7V2, continuous
                vv
clus             ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  TP53 MUTATED         0                  0    1     1      0     1     0
  TP53 WILD-TYPE       2                  2    3     2      1     1     1
                vv
clus             OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  TP53 MUTATED                       0             0               1
  TP53 WILD-TYPE                     1             1               2
                vv
clus             SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  TP53 MUTATED                                               0       0       0
  TP53 WILD-TYPE                                             1       2       2
D7V3, multiclass
                                               clus
vv                                              TP53 MUTATED TP53 WILD-TYPE
  ADRENAL                                                  0              2
  ASCITES/PERITONEUM                                       0              2
  BONE                                                     1              3
  BRAIN                                                    1              2
  BREAST                                                   0              1
  COLON                                                    1              1
  LIVER                                                    0              1
  OTHER EXTRANODAL SITE                                    0              1
  PAROTID GLAND                                            0              1
  SMALL INTESTINE                                          1              2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)            0              1
  STOMACH                                                  0              2
  THYROID                                                  0              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, binary
                cls
clus              0  1
  TP53 MUTATED    5  0
  TP53 WILD-TYPE 21 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      5    0
  TP53 WILD-TYPE   21   22
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            5             21
  MALE              0             22
[1] 2 2
[1] FALSE
D7V5, binary
                cls
clus              0  1
  TP53 MUTATED    5  0
  TP53 WILD-TYPE 35  7
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      5    0
  TP53 WILD-TYPE   35    7
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO             5             35
  YES            0              7
[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                                                                                37
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  TP53 MUTATED                          1                                  0
  TP53 WILD-TYPE                        2                                  4
D7V6, 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                                                           0
                                                                                   clus
vv                                                                                  TP53 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             37
  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
  TP53 MUTATED       2                         0     3
  TP53 WILD-TYPE    16                         1    26
D7V7, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                2             16
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                3             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                cls
clus              0  1
  TP53 MUTATED    2  3
  TP53 WILD-TYPE 10 33
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      2    3
  TP53 WILD-TYPE   10   33
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                2             10
  NOT HISPANIC OR LATINO            3             33
[1] 2 2
[1] FALSE

Clustering(8) Variable = TNFAIP3 MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  TNFAIP3 MUTATED    5  2
  TNFAIP3 WILD-TYPE 33  7
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
                7                40 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
                2                 7 
$`TNFAIP3 MUTATED`
TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-A7CR TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6325 
       18.18        35.54        10.29        12.66        41.16        51.98 
TCGA-GS-A9TZ 
       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-G8-6326 
       27.35        22.32         9.80        26.01        31.96        70.06 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 
      211.23        19.56       116.81       196.60       150.51        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 
            51.98            211.23 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
           25.150            29.225 
[1] "10.3 - 52.0 (25.1)" "0.0 - 211.2 (29.2)"
[1] "hr=" "2.4"
D8V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  TNFAIP3 MUTATED         1                  1    0     1      0     0     0
  TNFAIP3 WILD-TYPE       1                  1    4     2      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  TNFAIP3 MUTATED                       0             0               0
  TNFAIP3 WILD-TYPE                     1             1               3
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  TNFAIP3 MUTATED                                               0       0
  TNFAIP3 WILD-TYPE                                             1       2
                   vv
clus                THYROID
  TNFAIP3 MUTATED         0
  TNFAIP3 WILD-TYPE       2
D8V3, multiclass
                                               clus
vv                                              TNFAIP3 MUTATED
  ADRENAL                                                     1
  ASCITES/PERITONEUM                                          1
  BONE                                                        0
  BRAIN                                                       1
  BREAST                                                      0
  COLON                                                       0
  LIVER                                                       0
  OTHER EXTRANODAL SITE                                       0
  PAROTID GLAND                                               0
  SMALL INTESTINE                                             0
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)               0
  STOMACH                                                     0
  THYROID                                                     0
                                               clus
vv                                              TNFAIP3 WILD-TYPE
  ADRENAL                                                       1
  ASCITES/PERITONEUM                                            1
  BONE                                                          4
  BRAIN                                                         2
  BREAST                                                        1
  COLON                                                         2
  LIVER                                                         1
  OTHER EXTRANODAL SITE                                         1
  PAROTID GLAND                                                 1
  SMALL INTESTINE                                               3
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                 1
  STOMACH                                                       2
  THYROID                                                       2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, binary
                   cls
clus                 0  1
  TNFAIP3 MUTATED    3  4
  TNFAIP3 WILD-TYPE 23 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED      3    4
  TNFAIP3 WILD-TYPE   23   18
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  FEMALE               3                23
  MALE                 4                18
[1] 2 2
[1] FALSE
D8V5, binary
                   cls
clus                 0  1
  TNFAIP3 MUTATED    6  1
  TNFAIP3 WILD-TYPE 34  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED      6    1
  TNFAIP3 WILD-TYPE   34    6
     clus
vv    TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  NO                6                34
  YES               1                 6
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  TNFAIP3 MUTATED                                                                                   5
  TNFAIP3 WILD-TYPE                                                                                36
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  TNFAIP3 MUTATED                          0                                  2
  TNFAIP3 WILD-TYPE                        3                                  2
D8V6, multiclass
                                                                                   clus
vv                                                                                  TNFAIP3 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                                                                                  TNFAIP3 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                36
  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     3
  TNFAIP3 WILD-TYPE    15                         0    26
D8V7, multiclass
                           clus
vv                          TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                   3                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                   cls
clus                 0  1
  TNFAIP3 MUTATED    1  6
  TNFAIP3 WILD-TYPE 11 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED      1    6
  TNFAIP3 WILD-TYPE   11   30
                        clus
vv                       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               6                30
[1] 2 2
[1] FALSE

Clustering(9) Variable = TMSB4X MUTATION ANALYSIS
D9V1, survival
                  sevent
clus2               0  1
  TMSB4X MUTATED    4  2
  TMSB4X WILD-TYPE 34  7
  TMSB4X MUTATED TMSB4X WILD-TYPE 
               6               41 
  TMSB4X MUTATED TMSB4X WILD-TYPE 
               2                7 
$`TMSB4X MUTATED`
TCGA-FA-A6HN TCGA-FF-8042 TCGA-FF-8062 TCGA-G8-6907 TCGA-GS-A9TV TCGA-GS-A9TW 
        1.91        31.10        22.32        19.56        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-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 TCGA-G8-6914 
       41.16        51.98        70.06       211.23       116.81       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      150.51        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           211.23 
  TMSB4X MUTATED TMSB4X WILD-TYPE 
           23.16            31.73 
[1] "1.9 - 53.2 (23.2)"  "0.0 - 211.2 (31.7)"
[1] "hr=" "3.1"
D9V2, continuous
                  vv
clus               ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  TMSB4X MUTATED         0                  0    0     0      0     0     0
  TMSB4X WILD-TYPE       2                  2    4     3      1     2     1
                  vv
clus               OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  TMSB4X MUTATED                       0             0               0
  TMSB4X WILD-TYPE                     1             1               3
                  vv
clus               SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  TMSB4X MUTATED                                               0       0
  TMSB4X WILD-TYPE                                             1       2
                  vv
clus               THYROID
  TMSB4X MUTATED         1
  TMSB4X WILD-TYPE       1
D9V3, multiclass
[1] "Remove cluster labels:" "TMSB4X MUTATED"        
clus
  TMSB4X MUTATED TMSB4X WILD-TYPE 
               1               24 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A4XK       TCGA-FA-A7DS 
"TMSB4X WILD-TYPE" "TMSB4X WILD-TYPE" "TMSB4X WILD-TYPE" "TMSB4X WILD-TYPE" 
      TCGA-FA-A82F       TCGA-FF-8043       TCGA-FF-8061       TCGA-FF-A7CQ 
"TMSB4X WILD-TYPE" "TMSB4X WILD-TYPE" "TMSB4X WILD-TYPE" "TMSB4X WILD-TYPE" 
      TCGA-FF-A7CR       TCGA-FF-A7CW       TCGA-FF-A7CX       TCGA-FM-8000 
"TMSB4X WILD-TYPE" "TMSB4X WILD-TYPE" "TMSB4X WILD-TYPE" "TMSB4X WILD-TYPE" 
      TCGA-G8-6324       TCGA-G8-6326       TCGA-G8-6906       TCGA-GR-7351 
"TMSB4X WILD-TYPE" "TMSB4X WILD-TYPE" "TMSB4X WILD-TYPE" "TMSB4X WILD-TYPE" 
      TCGA-GR-A4D4       TCGA-GR-A4D5       TCGA-GR-A4D9       TCGA-GS-A9TT 
"TMSB4X WILD-TYPE" "TMSB4X WILD-TYPE" "TMSB4X WILD-TYPE" "TMSB4X WILD-TYPE" 
      TCGA-RQ-A68N       TCGA-RQ-A6JB       TCGA-RQ-AAAT       TCGA-VB-A8QN 
"TMSB4X WILD-TYPE" "TMSB4X WILD-TYPE" "TMSB4X WILD-TYPE" "TMSB4X WILD-TYPE" 
D9V4, binary
                  cls
clus                0  1
  TMSB4X MUTATED    5  1
  TMSB4X WILD-TYPE 21 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMSB4X MUTATED      5    1
  TMSB4X WILD-TYPE   21   21
        clus
vv       TMSB4X MUTATED TMSB4X WILD-TYPE
  FEMALE              5               21
  MALE                1               21
[1] 2 2
[1] FALSE
D9V5, binary
                  cls
clus                0  1
  TMSB4X MUTATED    4  2
  TMSB4X WILD-TYPE 36  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMSB4X MUTATED      4    2
  TMSB4X WILD-TYPE   36    5
     clus
vv    TMSB4X MUTATED TMSB4X WILD-TYPE
  NO               4               36
  YES              2                5
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  TMSB4X MUTATED                                                                                   4
  TMSB4X WILD-TYPE                                                                                37
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  TMSB4X MUTATED                          0                                  2
  TMSB4X WILD-TYPE                        3                                  2
D9V6, multiclass
                                                                                   clus
vv                                                                                  TMSB4X 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                                                                                  TMSB4X WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               37
  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     3
  TMSB4X WILD-TYPE    15                         1    26
D9V7, multiclass
                           clus
vv                          TMSB4X MUTATED TMSB4X WILD-TYPE
  ASIAN                                  3               15
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  3               26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                  cls
clus                0  1
  TMSB4X MUTATED    2  4
  TMSB4X WILD-TYPE 10 32
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMSB4X MUTATED      2    4
  TMSB4X WILD-TYPE   10   32
                        clus
vv                       TMSB4X MUTATED TMSB4X WILD-TYPE
  HISPANIC OR LATINO                  2               10
  NOT HISPANIC OR LATINO              4               32
[1] 2 2
[1] FALSE

Clustering(10) Variable = APLF MUTATION ANALYSIS
D10V1, survival
                sevent
clus2             0  1
  APLF MUTATED    1  2
  APLF WILD-TYPE 37  7
  APLF MUTATED APLF WILD-TYPE 
             3             44 
  APLF MUTATED APLF WILD-TYPE 
             2              7 
$`APLF MUTATED`
TCGA-G8-6906 TCGA-G8-6909 TCGA-GR-7351 
      211.23       116.81       150.51 

$`APLF 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-G8-6325 TCGA-G8-6326 
       26.01        12.66        31.96        41.16        51.98        70.06 
TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
       19.56       196.60        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-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  APLF MUTATED APLF WILD-TYPE 
        116.81           0.03 
  APLF MUTATED APLF WILD-TYPE 
        211.23         196.60 
  APLF MUTATED APLF WILD-TYPE 
        150.51          25.96 
[1] "116.8 - 211.2 (150.5)" "0.0 - 196.6 (26.0)"   
[1] "hr=" "1.4"
D10V2, continuous
                vv
clus             ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  APLF MUTATED         0                  0    0     0      0     0     0
  APLF WILD-TYPE       2                  2    4     3      1     2     1
                vv
clus             OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  APLF MUTATED                       1             0               0
  APLF WILD-TYPE                     0             1               3
                vv
clus             SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  APLF MUTATED                                               0       0       1
  APLF WILD-TYPE                                             1       2       1
D10V3, multiclass
[1] "Remove cluster labels:" "APLF MUTATED"          
clus
  APLF MUTATED APLF WILD-TYPE 
             2             23 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A7DS 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FA-A82F     TCGA-FF-8043     TCGA-FF-8061     TCGA-FF-8062 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FF-A7CQ     TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-FM-8000     TCGA-G8-6324     TCGA-G8-6326     TCGA-GR-A4D4 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-GR-A4D5     TCGA-GR-A4D9     TCGA-GS-A9TT     TCGA-RQ-A68N 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
    TCGA-RQ-A6JB     TCGA-RQ-AAAT     TCGA-VB-A8QN 
"APLF WILD-TYPE" "APLF WILD-TYPE" "APLF WILD-TYPE" 
D10V4, binary
                cls
clus              0  1
  APLF MUTATED    1  2
  APLF WILD-TYPE 25 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  APLF MUTATED      1    2
  APLF WILD-TYPE   25   20
        clus
vv       APLF MUTATED APLF WILD-TYPE
  FEMALE            1             25
  MALE              2             20
[1] 2 2
[1] FALSE
D10V5, binary
                cls
clus              0  1
  APLF MUTATED    2  1
  APLF WILD-TYPE 38  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  APLF MUTATED      2    1
  APLF WILD-TYPE   38    6
     clus
vv    APLF MUTATED APLF WILD-TYPE
  NO             2             38
  YES            1              6
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  APLF MUTATED                                                                                   3
  APLF WILD-TYPE                                                                                38
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  APLF MUTATED                          0                                  0
  APLF WILD-TYPE                        3                                  4
D10V6, multiclass
                                                                                   clus
vv                                                                                  APLF 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                                                                                  APLF WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             38
  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
  APLF MUTATED       0                         0     3
  APLF WILD-TYPE    18                         1    26
D10V7, multiclass
                           clus
vv                          APLF MUTATED APLF WILD-TYPE
  ASIAN                                0             18
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                3             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                cls
clus              0  1
  APLF MUTATED    0  3
  APLF WILD-TYPE 12 33
[1] "tbl2"
                cls
clus             [,1] [,2]
  APLF MUTATED      0    3
  APLF WILD-TYPE   12   33
                        clus
vv                       APLF MUTATED APLF WILD-TYPE
  HISPANIC OR LATINO                0             12
  NOT HISPANIC OR LATINO            3             33
[1] 2 2
[1] FALSE

Clustering(11) Variable = RHPN2 MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2              0  1
  RHPN2 MUTATED    4  3
  RHPN2 WILD-TYPE 34  6
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              7              40 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              3               6 
$`RHPN2 MUTATED`
TCGA-FF-8046 TCGA-FF-8061 TCGA-G8-6324 TCGA-G8-6906 TCGA-G8-6907 TCGA-GR-7351 
       24.69        27.35        41.16       211.23        19.56       150.51 
TCGA-GS-A9TU 
      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-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8047 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
        4.14        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7353 
       31.96        51.98        70.06       116.81       196.60        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 
          19.56            0.03 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
         211.23          196.60 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
          41.16           25.96 
[1] "19.6 - 211.2 (41.2)" "0.0 - 196.6 (26.0)" 
[1] "hr=" "1.1"
D11V2, continuous
                 vv
clus              ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  RHPN2 MUTATED         0                  1    0     0      0     0     0
  RHPN2 WILD-TYPE       2                  1    4     3      1     2     1
                 vv
clus              OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  RHPN2 MUTATED                       1             0               1
  RHPN2 WILD-TYPE                     0             1               2
                 vv
clus              SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  RHPN2 MUTATED                                               0       0       1
  RHPN2 WILD-TYPE                                             1       2       1
D11V3, multiclass
                                               clus
vv                                              RHPN2 MUTATED RHPN2 WILD-TYPE
  ADRENAL                                                   0               2
  ASCITES/PERITONEUM                                        1               1
  BONE                                                      0               4
  BRAIN                                                     0               3
  BREAST                                                    0               1
  COLON                                                     0               2
  LIVER                                                     0               1
  OTHER EXTRANODAL SITE                                     1               0
  PAROTID GLAND                                             0               1
  SMALL INTESTINE                                           1               2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)             0               1
  STOMACH                                                   0               2
  THYROID                                                   1               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V4, binary
                 cls
clus               0  1
  RHPN2 MUTATED    3  4
  RHPN2 WILD-TYPE 23 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED      3    4
  RHPN2 WILD-TYPE   23   18
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  FEMALE             3              23
  MALE               4              18
[1] 2 2
[1] FALSE
D11V5, binary
                 cls
clus               0  1
  RHPN2 MUTATED    5  2
  RHPN2 WILD-TYPE 35  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED      5    2
  RHPN2 WILD-TYPE   35    5
     clus
vv    RHPN2 MUTATED RHPN2 WILD-TYPE
  NO              5              35
  YES             2               5
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  RHPN2 MUTATED                                                                                   7
  RHPN2 WILD-TYPE                                                                                34
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  RHPN2 MUTATED                          0                                  0
  RHPN2 WILD-TYPE                        3                                  4
D11V6, multiclass
                                                                                   clus
vv                                                                                  RHPN2 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                                                                                  RHPN2 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              34
  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
  RHPN2 MUTATED       2                         1     4
  RHPN2 WILD-TYPE    16                         0    25
D11V7, multiclass
                           clus
vv                          RHPN2 MUTATED RHPN2 WILD-TYPE
  ASIAN                                 2              16
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 4              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
                 cls
clus               0  1
  RHPN2 MUTATED    1  6
  RHPN2 WILD-TYPE 11 30
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED      1    6
  RHPN2 WILD-TYPE   11   30
                        clus
vv                       RHPN2 MUTATED RHPN2 WILD-TYPE
  HISPANIC OR LATINO                 1              11
  NOT HISPANIC OR LATINO             6              30
[1] 2 2
[1] FALSE

Clustering(12) Variable = CIITA MUTATION ANALYSIS
D12V1, survival
                 sevent
clus2              0  1
  CIITA MUTATED    4  1
  CIITA WILD-TYPE 34  8
  CIITA MUTATED CIITA WILD-TYPE 
              5              42 
  CIITA MUTATED CIITA WILD-TYPE 
              1               8 
$`CIITA MUTATED`
TCGA-FA-A7Q1 TCGA-FF-8041 TCGA-GR-7351 TCGA-GR-A4D9 TCGA-GS-A9TT 
        8.15        35.54       150.51        57.17        38.24 

$`CIITA 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-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-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       31.96        41.16        51.98        70.06       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      116.81       196.60        98.07        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 

  CIITA MUTATED CIITA WILD-TYPE 
           8.15            0.03 
  CIITA MUTATED CIITA WILD-TYPE 
         150.51          211.23 
  CIITA MUTATED CIITA WILD-TYPE 
          38.24           25.96 
[1] "8.2 - 150.5 (38.2)" "0.0 - 211.2 (26.0)"
[1] "hr=" "1"  
D12V2, continuous
                 vv
clus              ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  CIITA MUTATED         0                  0    1     0      0     0     0
  CIITA WILD-TYPE       2                  2    3     3      1     2     1
                 vv
clus              OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  CIITA MUTATED                       0             0               0
  CIITA WILD-TYPE                     1             1               3
                 vv
clus              SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  CIITA MUTATED                                               1       0       1
  CIITA WILD-TYPE                                             0       2       1
D12V3, multiclass
                                               clus
vv                                              CIITA MUTATED CIITA WILD-TYPE
  ADRENAL                                                   0               2
  ASCITES/PERITONEUM                                        0               2
  BONE                                                      1               3
  BRAIN                                                     0               3
  BREAST                                                    0               1
  COLON                                                     0               2
  LIVER                                                     0               1
  OTHER EXTRANODAL SITE                                     0               1
  PAROTID GLAND                                             0               1
  SMALL INTESTINE                                           0               3
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)             1               0
  STOMACH                                                   0               2
  THYROID                                                   1               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, binary
                 cls
clus               0  1
  CIITA MUTATED    4  1
  CIITA WILD-TYPE 22 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CIITA MUTATED      4    1
  CIITA WILD-TYPE   22   21
        clus
vv       CIITA MUTATED CIITA WILD-TYPE
  FEMALE             4              22
  MALE               1              21
[1] 2 2
[1] FALSE
D12V5, binary
                 cls
clus               0  1
  CIITA MUTATED    3  2
  CIITA WILD-TYPE 37  5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CIITA MUTATED      3    2
  CIITA WILD-TYPE   37    5
     clus
vv    CIITA MUTATED CIITA WILD-TYPE
  NO              3              37
  YES             2               5
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  CIITA MUTATED                                                                                   4
  CIITA WILD-TYPE                                                                                37
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  CIITA MUTATED                          0                                  1
  CIITA WILD-TYPE                        3                                  3
D12V6, multiclass
                                                                                   clus
vv                                                                                  CIITA 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                                                                                  CIITA WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              37
  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
  CIITA MUTATED       2                         0     3
  CIITA WILD-TYPE    16                         1    26
D12V7, multiclass
                           clus
vv                          CIITA MUTATED CIITA WILD-TYPE
  ASIAN                                 2              16
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 3              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                 cls
clus               0  1
  CIITA MUTATED    1  4
  CIITA WILD-TYPE 11 32
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CIITA MUTATED      1    4
  CIITA WILD-TYPE   11   32
                        clus
vv                       CIITA MUTATED CIITA WILD-TYPE
  HISPANIC OR LATINO                 1              11
  NOT HISPANIC OR LATINO             4              32
[1] 2 2
[1] FALSE

Clustering(13) Variable = KDR MUTATION ANALYSIS
D13V1, survival
               sevent
clus2            0  1
  KDR MUTATED    3  1
  KDR WILD-TYPE 35  8
  KDR MUTATED KDR WILD-TYPE 
            4            43 
  KDR MUTATED KDR WILD-TYPE 
            1             8 
$`KDR MUTATED`
TCGA-G8-6326 TCGA-G8-6909 TCGA-GR-A4D5 TCGA-RQ-A68N 
       70.06       116.81        42.71        25.91 

$`KDR 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-G8-6325 TCGA-G8-6906 
       26.01        12.66        31.96        41.16        51.98       211.23 
TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
       19.56       196.60       150.51        98.07        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-A6JB 
       45.14       109.58        25.15       111.58        12.85         0.03 
TCGA-RQ-AAAT 
        0.56 

  KDR MUTATED KDR WILD-TYPE 
        25.91          0.03 
  KDR MUTATED KDR WILD-TYPE 
       116.81        211.23 
  KDR MUTATED KDR WILD-TYPE 
       56.385        26.010 
[1] "25.9 - 116.8 (56.4)" "0.0 - 211.2 (26.0)" 
[1] "hr=" "1"  
D13V2, continuous
               vv
clus            ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  KDR MUTATED         0                  1    1     1      0     0     0
  KDR WILD-TYPE       2                  1    3     2      1     2     1
               vv
clus            OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  KDR MUTATED                       0             0               0
  KDR WILD-TYPE                     1             1               3
               vv
clus            SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  KDR MUTATED                                               0       0       0
  KDR WILD-TYPE                                             1       2       2
D13V3, multiclass
                                               clus
vv                                              KDR MUTATED KDR WILD-TYPE
  ADRENAL                                                 0             2
  ASCITES/PERITONEUM                                      1             1
  BONE                                                    1             3
  BRAIN                                                   1             2
  BREAST                                                  0             1
  COLON                                                   0             2
  LIVER                                                   0             1
  OTHER EXTRANODAL SITE                                   0             1
  PAROTID GLAND                                           0             1
  SMALL INTESTINE                                         0             3
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)           0             1
  STOMACH                                                 0             2
  THYROID                                                 0             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V4, binary
               cls
clus             0  1
  KDR MUTATED    1  3
  KDR WILD-TYPE 25 19
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED      1    3
  KDR WILD-TYPE   25   19
        clus
vv       KDR MUTATED KDR WILD-TYPE
  FEMALE           1            25
  MALE             3            19
[1] 2 2
[1] FALSE
D13V5, binary
               cls
clus             0  1
  KDR MUTATED    4  0
  KDR WILD-TYPE 36  7
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED      4    0
  KDR WILD-TYPE   36    7
     clus
vv    KDR MUTATED KDR WILD-TYPE
  NO            4            36
  YES           0             7
[1] 2 2
[1] FALSE
               vv
clus            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  KDR MUTATED                                                                                   3
  KDR WILD-TYPE                                                                                38
               vv
clus            PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  KDR MUTATED                          1                                  0
  KDR WILD-TYPE                        2                                  4
D13V6, multiclass
                                                                                   clus
vv                                                                                  KDR 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                                                                                  KDR WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)            38
  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
  KDR MUTATED       0                         0     4
  KDR WILD-TYPE    18                         1    25
D13V7, multiclass
                           clus
vv                          KDR MUTATED KDR WILD-TYPE
  ASIAN                               0            18
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                               4            25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
               cls
clus             0  1
  KDR MUTATED    1  3
  KDR WILD-TYPE 11 33
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED      1    3
  KDR WILD-TYPE   11   33
                        clus
vv                       KDR MUTATED KDR WILD-TYPE
  HISPANIC OR LATINO               1            11
  NOT HISPANIC OR LATINO           3            33
[1] 2 2
[1] FALSE

Clustering(14) Variable = CARD11 MUTATION ANALYSIS
D14V1, survival
                  sevent
clus2               0  1
  CARD11 MUTATED    9  1
  CARD11 WILD-TYPE 29  8
  CARD11 MUTATED CARD11 WILD-TYPE 
              10               37 
  CARD11 MUTATED CARD11 WILD-TYPE 
               1                8 
$`CARD11 MUTATED`
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8061 TCGA-FF-A7CW TCGA-FF-A7CX TCGA-G8-6324 
       35.54        31.10        27.35        26.01        12.66        41.16 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GS-A9TY 
      196.60       150.51        51.98       109.58 

$`CARD11 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-8046 TCGA-FF-8047 
        8.15        14.04        18.18        31.73        24.69         4.14 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FM-8000 TCGA-G8-6325 TCGA-G8-6326 
       22.32         9.80        10.29        31.96        51.98        70.06 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 
      211.23        19.56       116.81        98.07        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-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
       45.14        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  CARD11 MUTATED CARD11 WILD-TYPE 
           12.66             0.03 
  CARD11 MUTATED CARD11 WILD-TYPE 
          196.60           211.23 
  CARD11 MUTATED CARD11 WILD-TYPE 
           38.35            24.69 
[1] "12.7 - 196.6 (38.3)" "0.0 - 211.2 (24.7)" 
[1] "hr=" "2.7"
D14V2, continuous
                  vv
clus               ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  CARD11 MUTATED         1                  1    1     0      0     0     0
  CARD11 WILD-TYPE       1                  1    3     3      1     2     1
                  vv
clus               OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  CARD11 MUTATED                       0             1               1
  CARD11 WILD-TYPE                     1             0               2
                  vv
clus               SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  CARD11 MUTATED                                               0       0
  CARD11 WILD-TYPE                                             1       2
                  vv
clus               THYROID
  CARD11 MUTATED         1
  CARD11 WILD-TYPE       1
D14V3, multiclass
                                               clus
vv                                              CARD11 MUTATED CARD11 WILD-TYPE
  ADRENAL                                                    1                1
  ASCITES/PERITONEUM                                         1                1
  BONE                                                       1                3
  BRAIN                                                      0                3
  BREAST                                                     0                1
  COLON                                                      0                2
  LIVER                                                      0                1
  OTHER EXTRANODAL SITE                                      0                1
  PAROTID GLAND                                              1                0
  SMALL INTESTINE                                            1                2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)              0                1
  STOMACH                                                    0                2
  THYROID                                                    1                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V4, binary
                  cls
clus                0  1
  CARD11 MUTATED    6  4
  CARD11 WILD-TYPE 20 18
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD11 MUTATED      6    4
  CARD11 WILD-TYPE   20   18
        clus
vv       CARD11 MUTATED CARD11 WILD-TYPE
  FEMALE              6               20
  MALE                4               18
[1] 2 2
[1] FALSE
D14V5, binary
                  cls
clus                0  1
  CARD11 MUTATED    9  1
  CARD11 WILD-TYPE 31  6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD11 MUTATED      9    1
  CARD11 WILD-TYPE   31    6
     clus
vv    CARD11 MUTATED CARD11 WILD-TYPE
  NO               9               31
  YES              1                6
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  CARD11 MUTATED                                                                                   9
  CARD11 WILD-TYPE                                                                                32
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  CARD11 MUTATED                          0                                  1
  CARD11 WILD-TYPE                        3                                  3
D14V6, multiclass
                                                                                   clus
vv                                                                                  CARD11 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              9
  PRIMARY DLBCL OF THE CNS                                                                       0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                             1
                                                                                   clus
vv                                                                                  CARD11 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               32
  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
  CARD11 MUTATED       5                         1     4
  CARD11 WILD-TYPE    13                         0    25
D14V7, multiclass
                           clus
vv                          CARD11 MUTATED CARD11 WILD-TYPE
  ASIAN                                  5               13
  BLACK OR AFRICAN AMERICAN              1                0
  WHITE                                  4               25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, binary
                  cls
clus                0  1
  CARD11 MUTATED    1  9
  CARD11 WILD-TYPE 11 27
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD11 MUTATED      1    9
  CARD11 WILD-TYPE   11   27
                        clus
vv                       CARD11 MUTATED CARD11 WILD-TYPE
  HISPANIC OR LATINO                  1               11
  NOT HISPANIC OR LATINO              9               27
[1] 2 2
[1] FALSE

Clustering(15) Variable = EZH2 MUTATION ANALYSIS
D15V1, survival
                sevent
clus2             0  1
  EZH2 MUTATED    2  1
  EZH2 WILD-TYPE 36  8
  EZH2 MUTATED EZH2 WILD-TYPE 
             3             44 
  EZH2 MUTATED EZH2 WILD-TYPE 
             1              8 
$`EZH2 MUTATED`
TCGA-FM-8000 TCGA-G8-6325 TCGA-G8-6907 
       31.96        51.98        19.56 

$`EZH2 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-G8-6324 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 
       26.01        12.66        41.16        70.06       211.23       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        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-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  EZH2 MUTATED EZH2 WILD-TYPE 
         19.56           0.03 
  EZH2 MUTATED EZH2 WILD-TYPE 
         51.98         211.23 
  EZH2 MUTATED EZH2 WILD-TYPE 
         31.96          26.68 
[1] "19.6 - 52.0 (32.0)" "0.0 - 211.2 (26.7)"
[1] "hr=" "2.1"
D15V2, continuous
                vv
clus             ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  EZH2 MUTATED         0                  0    0     0      0     1     0
  EZH2 WILD-TYPE       2                  2    4     3      1     1     1
                vv
clus             OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  EZH2 MUTATED                       0             0               0
  EZH2 WILD-TYPE                     1             1               3
                vv
clus             SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  EZH2 MUTATED                                               0       0       0
  EZH2 WILD-TYPE                                             1       2       2
D15V3, multiclass
[1] "Remove cluster labels:" "EZH2 MUTATED"          
clus
  EZH2 MUTATED EZH2 WILD-TYPE 
             1             24 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A7DS 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-FA-A82F     TCGA-FF-8043     TCGA-FF-8061     TCGA-FF-8062 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-FF-A7CQ     TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-G8-6324     TCGA-G8-6326     TCGA-G8-6906     TCGA-GR-7351 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-GR-A4D4     TCGA-GR-A4D5     TCGA-GR-A4D9     TCGA-GS-A9TT 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-RQ-AAAT     TCGA-VB-A8QN 
"EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" "EZH2 WILD-TYPE" 
D15V4, binary
                cls
clus              0  1
  EZH2 MUTATED    2  1
  EZH2 WILD-TYPE 24 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED      2    1
  EZH2 WILD-TYPE   24   21
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  FEMALE            2             24
  MALE              1             21
[1] 2 2
[1] FALSE
D15V5, binary
                cls
clus              0  1
  EZH2 MUTATED    3  0
  EZH2 WILD-TYPE 37  7
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED      3    0
  EZH2 WILD-TYPE   37    7
     clus
vv    EZH2 MUTATED EZH2 WILD-TYPE
  NO             3             37
  YES            0              7
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  EZH2 MUTATED                                                                                   3
  EZH2 WILD-TYPE                                                                                38
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  EZH2 MUTATED                          0                                  0
  EZH2 WILD-TYPE                        3                                  4
D15V6, multiclass
                                                                                   clus
vv                                                                                  EZH2 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                                                                                  EZH2 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             38
  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
  EZH2 MUTATED       0                         0     3
  EZH2 WILD-TYPE    18                         1    26
D15V7, multiclass
                           clus
vv                          EZH2 MUTATED EZH2 WILD-TYPE
  ASIAN                                0             18
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                3             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                cls
clus              0  1
  EZH2 MUTATED    0  3
  EZH2 WILD-TYPE 12 33
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED      0    3
  EZH2 WILD-TYPE   12   33
                        clus
vv                       EZH2 MUTATED EZH2 WILD-TYPE
  HISPANIC OR LATINO                0             12
  NOT HISPANIC OR LATINO            3             33
[1] 2 2
[1] FALSE

Clustering(16) Variable = NFKBIE MUTATION ANALYSIS
D16V1, survival
                  sevent
clus2               0  1
  NFKBIE MUTATED    3  1
  NFKBIE WILD-TYPE 35  8
  NFKBIE MUTATED NFKBIE WILD-TYPE 
               4               43 
  NFKBIE MUTATED NFKBIE WILD-TYPE 
               1                8 
$`NFKBIE MUTATED`
TCGA-FF-8061 TCGA-G8-6325 TCGA-G8-6909 TCGA-GR-A4D6 
       27.35        51.98       116.81        43.86 

$`NFKBIE 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-G8-6324 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       12.66        31.96        41.16        70.06       211.23        19.56 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 
      196.60       150.51        98.07        51.98        42.71        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 

  NFKBIE MUTATED NFKBIE WILD-TYPE 
           27.35             0.03 
  NFKBIE MUTATED NFKBIE WILD-TYPE 
          116.81           211.23 
  NFKBIE MUTATED NFKBIE WILD-TYPE 
           47.92            25.91 
[1] "27.4 - 116.8 (47.9)" "0.0 - 211.2 (25.9)" 
[1] "hr=" "1"  
D16V2, continuous
                  vv
clus               ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  NFKBIE MUTATED         0                  0    0     0      0     0     0
  NFKBIE WILD-TYPE       2                  2    4     3      1     2     1
                  vv
clus               OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  NFKBIE MUTATED                       0             0               1
  NFKBIE WILD-TYPE                     1             1               2
                  vv
clus               SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  NFKBIE MUTATED                                               0       0
  NFKBIE WILD-TYPE                                             1       2
                  vv
clus               THYROID
  NFKBIE MUTATED         0
  NFKBIE WILD-TYPE       2
D16V3, multiclass
[1] "Remove cluster labels:" "NFKBIE MUTATED"        
clus
  NFKBIE MUTATED NFKBIE WILD-TYPE 
               1               24 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A4XK       TCGA-FA-A7DS 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-FA-A82F       TCGA-FF-8043       TCGA-FF-8062       TCGA-FF-A7CQ 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-FF-A7CR       TCGA-FF-A7CW       TCGA-FF-A7CX       TCGA-FM-8000 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-G8-6324       TCGA-G8-6326       TCGA-G8-6906       TCGA-GR-7351 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-GR-A4D4       TCGA-GR-A4D5       TCGA-GR-A4D9       TCGA-GS-A9TT 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-RQ-A68N       TCGA-RQ-A6JB       TCGA-RQ-AAAT       TCGA-VB-A8QN 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
D16V4, binary
                  cls
clus                0  1
  NFKBIE MUTATED    1  3
  NFKBIE WILD-TYPE 25 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIE MUTATED      1    3
  NFKBIE WILD-TYPE   25   19
        clus
vv       NFKBIE MUTATED NFKBIE WILD-TYPE
  FEMALE              1               25
  MALE                3               19
[1] 2 2
[1] FALSE
D16V5, binary
                  cls
clus                0  1
  NFKBIE MUTATED    4  0
  NFKBIE WILD-TYPE 36  7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIE MUTATED      4    0
  NFKBIE WILD-TYPE   36    7
     clus
vv    NFKBIE MUTATED NFKBIE WILD-TYPE
  NO               4               36
  YES              0                7
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  NFKBIE MUTATED                                                                                   4
  NFKBIE WILD-TYPE                                                                                37
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  NFKBIE MUTATED                          0                                  0
  NFKBIE WILD-TYPE                        3                                  4
D16V6, multiclass
                                                                                   clus
vv                                                                                  NFKBIE 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                                                                                  NFKBIE WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               37
  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
  NFKBIE MUTATED       2                         0     2
  NFKBIE WILD-TYPE    16                         1    27
D16V7, multiclass
                           clus
vv                          NFKBIE MUTATED NFKBIE WILD-TYPE
  ASIAN                                  2               16
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  2               27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                  cls
clus                0  1
  NFKBIE MUTATED    0  4
  NFKBIE WILD-TYPE 12 32
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIE MUTATED      0    4
  NFKBIE WILD-TYPE   12   32
                        clus
vv                       NFKBIE MUTATED NFKBIE WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              4               32
[1] 2 2
[1] FALSE

Clustering(17) Variable = MLH1 MUTATION ANALYSIS
D17V1, survival
                sevent
clus2             0  1
  MLH1 MUTATED    2  1
  MLH1 WILD-TYPE 36  8
  MLH1 MUTATED MLH1 WILD-TYPE 
             3             44 
  MLH1 MUTATED MLH1 WILD-TYPE 
             1              8 
$`MLH1 MUTATED`
TCGA-G8-6325 TCGA-G8-6906 TCGA-GR-7351 
       51.98       211.23       150.51 

$`MLH1 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-G8-6326 TCGA-G8-6907 
       26.01        12.66        31.96        41.16        70.06        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      116.81       196.60        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-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  MLH1 MUTATED MLH1 WILD-TYPE 
         51.98           0.03 
  MLH1 MUTATED MLH1 WILD-TYPE 
        211.23         196.60 
  MLH1 MUTATED MLH1 WILD-TYPE 
        150.51          25.96 
[1] "52.0 - 211.2 (150.5)" "0.0 - 196.6 (26.0)"  
[1] "hr="   "1e+08"
D17V2, continuous
                vv
clus             ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  MLH1 MUTATED         0                  0    0     0      0     0     0
  MLH1 WILD-TYPE       2                  2    4     3      1     2     1
                vv
clus             OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  MLH1 MUTATED                       1             0               0
  MLH1 WILD-TYPE                     0             1               3
                vv
clus             SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  MLH1 MUTATED                                               0       0       1
  MLH1 WILD-TYPE                                             1       2       1
D17V3, multiclass
[1] "Remove cluster labels:" "MLH1 MUTATED"          
clus
  MLH1 MUTATED MLH1 WILD-TYPE 
             2             23 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A7DS 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FA-A82F     TCGA-FF-8043     TCGA-FF-8061     TCGA-FF-8062 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FF-A7CQ     TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-FM-8000     TCGA-G8-6324     TCGA-G8-6326     TCGA-GR-A4D4 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-GR-A4D5     TCGA-GR-A4D9     TCGA-GS-A9TT     TCGA-RQ-A68N 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
    TCGA-RQ-A6JB     TCGA-RQ-AAAT     TCGA-VB-A8QN 
"MLH1 WILD-TYPE" "MLH1 WILD-TYPE" "MLH1 WILD-TYPE" 
D17V4, binary
                cls
clus              0  1
  MLH1 MUTATED    1  2
  MLH1 WILD-TYPE 25 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED      1    2
  MLH1 WILD-TYPE   25   20
        clus
vv       MLH1 MUTATED MLH1 WILD-TYPE
  FEMALE            1             25
  MALE              2             20
[1] 2 2
[1] FALSE
D17V5, binary
                cls
clus              0  1
  MLH1 MUTATED    2  1
  MLH1 WILD-TYPE 38  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED      2    1
  MLH1 WILD-TYPE   38    6
     clus
vv    MLH1 MUTATED MLH1 WILD-TYPE
  NO             2             38
  YES            1              6
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  MLH1 MUTATED                                                                                   3
  MLH1 WILD-TYPE                                                                                38
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  MLH1 MUTATED                          0                                  0
  MLH1 WILD-TYPE                        3                                  4
D17V6, multiclass
                                                                                   clus
vv                                                                                  MLH1 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                                                                                  MLH1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             38
  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
  MLH1 MUTATED       0                         0     3
  MLH1 WILD-TYPE    18                         1    26
D17V7, multiclass
                           clus
vv                          MLH1 MUTATED MLH1 WILD-TYPE
  ASIAN                                0             18
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                3             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, binary
                cls
clus              0  1
  MLH1 MUTATED    0  3
  MLH1 WILD-TYPE 12 33
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED      0    3
  MLH1 WILD-TYPE   12   33
                        clus
vv                       MLH1 MUTATED MLH1 WILD-TYPE
  HISPANIC OR LATINO                0             12
  NOT HISPANIC OR LATINO            3             33
[1] 2 2
[1] FALSE

Clustering(18) Variable = FAS MUTATION ANALYSIS
D18V1, survival
               sevent
clus2            0  1
  FAS MUTATED    2  3
  FAS WILD-TYPE 36  6
  FAS MUTATED FAS WILD-TYPE 
            5            42 
  FAS MUTATED FAS WILD-TYPE 
            3             6 
$`FAS MUTATED`
TCGA-FA-A7Q1 TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-A4D4 TCGA-GS-A9U3 
        8.15        19.56       116.81        51.98       111.58 

$`FAS 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-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       12.66        31.96        41.16        51.98        70.06       211.23 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      196.60       150.51        98.07        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-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
      109.58        25.15        12.85        25.91         0.03         0.56 

  FAS MUTATED FAS WILD-TYPE 
         8.15          0.03 
  FAS MUTATED FAS WILD-TYPE 
       116.81        211.23 
  FAS MUTATED FAS WILD-TYPE 
        51.98         26.68 
[1] "8.2 - 116.8 (52.0)" "0.0 - 211.2 (26.7)"
[1] "hr=" "4.1"
D18V2, continuous
               vv
clus            ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  FAS MUTATED         0                  0    1     0      0     0     0
  FAS WILD-TYPE       2                  2    3     3      1     2     1
               vv
clus            OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  FAS MUTATED                       0             0               0
  FAS WILD-TYPE                     1             1               3
               vv
clus            SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  FAS MUTATED                                               0       0       0
  FAS WILD-TYPE                                             1       2       2
D18V3, multiclass
[1] "Remove cluster labels:" "FAS MUTATED"           
clus
  FAS MUTATED FAS WILD-TYPE 
            1            24 
   TCGA-FA-8693    TCGA-FA-A4BB    TCGA-FA-A4XK    TCGA-FA-A7DS    TCGA-FA-A82F 
"FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" 
   TCGA-FF-8043    TCGA-FF-8061    TCGA-FF-8062    TCGA-FF-A7CQ    TCGA-FF-A7CR 
"FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" 
   TCGA-FF-A7CW    TCGA-FF-A7CX    TCGA-FM-8000    TCGA-G8-6324    TCGA-G8-6326 
"FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" 
   TCGA-G8-6906    TCGA-GR-7351    TCGA-GR-A4D5    TCGA-GR-A4D9    TCGA-GS-A9TT 
"FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" 
   TCGA-RQ-A68N    TCGA-RQ-A6JB    TCGA-RQ-AAAT    TCGA-VB-A8QN 
"FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" "FAS WILD-TYPE" 
D18V4, binary
               cls
clus             0  1
  FAS MUTATED    4  1
  FAS WILD-TYPE 22 21
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAS MUTATED      4    1
  FAS WILD-TYPE   22   21
        clus
vv       FAS MUTATED FAS WILD-TYPE
  FEMALE           4            22
  MALE             1            21
[1] 2 2
[1] FALSE
D18V5, binary
               cls
clus             0  1
  FAS MUTATED    5  0
  FAS WILD-TYPE 35  7
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAS MUTATED      5    0
  FAS WILD-TYPE   35    7
     clus
vv    FAS MUTATED FAS WILD-TYPE
  NO            5            35
  YES           0             7
[1] 2 2
[1] FALSE
               vv
clus            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  FAS MUTATED                                                                                   5
  FAS WILD-TYPE                                                                                36
               vv
clus            PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  FAS MUTATED                          0                                  0
  FAS WILD-TYPE                        3                                  4
D18V6, multiclass
                                                                                   clus
vv                                                                                  FAS 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                                                                                  FAS WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)            36
  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
  FAS MUTATED       1                         0     4
  FAS WILD-TYPE    17                         1    25
D18V7, multiclass
                           clus
vv                          FAS MUTATED FAS WILD-TYPE
  ASIAN                               1            17
  BLACK OR AFRICAN AMERICAN           0             1
  WHITE                               4            25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
               cls
clus             0  1
  FAS MUTATED    1  4
  FAS WILD-TYPE 11 32
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAS MUTATED      1    4
  FAS WILD-TYPE   11   32
                        clus
vv                       FAS MUTATED FAS WILD-TYPE
  HISPANIC OR LATINO               1            11
  NOT HISPANIC OR LATINO           4            32
[1] 2 2
[1] FALSE

Clustering(19) Variable = ENOX1 MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2              0  1
  ENOX1 MUTATED    2  2
  ENOX1 WILD-TYPE 36  7
  ENOX1 MUTATED ENOX1 WILD-TYPE 
              4              43 
  ENOX1 MUTATED ENOX1 WILD-TYPE 
              2               7 
$`ENOX1 MUTATED`
TCGA-FF-8042 TCGA-G8-6324 TCGA-G8-6906 TCGA-GS-A9TZ 
       31.10        41.16       211.23        25.15 

$`ENOX1 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-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-G8-6325 TCGA-G8-6326 TCGA-G8-6907 TCGA-G8-6909 
       12.66        31.96        51.98        70.06        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        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-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
       45.14       109.58       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  ENOX1 MUTATED ENOX1 WILD-TYPE 
          25.15            0.03 
  ENOX1 MUTATED ENOX1 WILD-TYPE 
         211.23          196.60 
  ENOX1 MUTATED ENOX1 WILD-TYPE 
          36.13           26.01 
[1] "25.1 - 211.2 (36.1)" "0.0 - 196.6 (26.0)" 
[1] "hr=" "1.1"
D19V2, continuous
                 vv
clus              ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  ENOX1 MUTATED         0                  1    0     0      0     0     0
  ENOX1 WILD-TYPE       2                  1    4     3      1     2     1
                 vv
clus              OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  ENOX1 MUTATED                       1             0               0
  ENOX1 WILD-TYPE                     0             1               3
                 vv
clus              SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  ENOX1 MUTATED                                               0       0       0
  ENOX1 WILD-TYPE                                             1       2       2
D19V3, multiclass
[1] "Remove cluster labels:" "ENOX1 MUTATED"         
clus
  ENOX1 MUTATED ENOX1 WILD-TYPE 
              2              23 
     TCGA-FA-8693      TCGA-FA-A4BB      TCGA-FA-A4XK      TCGA-FA-A7DS 
"ENOX1 WILD-TYPE" "ENOX1 WILD-TYPE" "ENOX1 WILD-TYPE" "ENOX1 WILD-TYPE" 
     TCGA-FA-A82F      TCGA-FF-8043      TCGA-FF-8061      TCGA-FF-8062 
"ENOX1 WILD-TYPE" "ENOX1 WILD-TYPE" "ENOX1 WILD-TYPE" "ENOX1 WILD-TYPE" 
     TCGA-FF-A7CQ      TCGA-FF-A7CR      TCGA-FF-A7CW      TCGA-FF-A7CX 
"ENOX1 WILD-TYPE" "ENOX1 WILD-TYPE" "ENOX1 WILD-TYPE" "ENOX1 WILD-TYPE" 
     TCGA-FM-8000      TCGA-G8-6326      TCGA-GR-7351      TCGA-GR-A4D4 
"ENOX1 WILD-TYPE" "ENOX1 WILD-TYPE" "ENOX1 WILD-TYPE" "ENOX1 WILD-TYPE" 
     TCGA-GR-A4D5      TCGA-GR-A4D9      TCGA-GS-A9TT      TCGA-RQ-A68N 
"ENOX1 WILD-TYPE" "ENOX1 WILD-TYPE" "ENOX1 WILD-TYPE" "ENOX1 WILD-TYPE" 
     TCGA-RQ-A6JB      TCGA-RQ-AAAT      TCGA-VB-A8QN 
"ENOX1 WILD-TYPE" "ENOX1 WILD-TYPE" "ENOX1 WILD-TYPE" 
D19V4, binary
                 cls
clus               0  1
  ENOX1 MUTATED    2  2
  ENOX1 WILD-TYPE 24 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENOX1 MUTATED      2    2
  ENOX1 WILD-TYPE   24   20
        clus
vv       ENOX1 MUTATED ENOX1 WILD-TYPE
  FEMALE             2              24
  MALE               2              20
[1] 2 2
[1] FALSE
D19V5, binary
                 cls
clus               0  1
  ENOX1 MUTATED    3  1
  ENOX1 WILD-TYPE 37  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENOX1 MUTATED      3    1
  ENOX1 WILD-TYPE   37    6
     clus
vv    ENOX1 MUTATED ENOX1 WILD-TYPE
  NO              3              37
  YES             1               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  ENOX1 MUTATED                                                                                   3
  ENOX1 WILD-TYPE                                                                                38
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  ENOX1 MUTATED                          0                                  1
  ENOX1 WILD-TYPE                        3                                  3
D19V6, multiclass
                                                                                   clus
vv                                                                                  ENOX1 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                                                                                  ENOX1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              38
  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
  ENOX1 MUTATED       1                         1     2
  ENOX1 WILD-TYPE    17                         0    27
D19V7, multiclass
                           clus
vv                          ENOX1 MUTATED ENOX1 WILD-TYPE
  ASIAN                                 1              17
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 2              27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                 cls
clus               0  1
  ENOX1 MUTATED    1  3
  ENOX1 WILD-TYPE 11 33
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENOX1 MUTATED      1    3
  ENOX1 WILD-TYPE   11   33
                        clus
vv                       ENOX1 MUTATED ENOX1 WILD-TYPE
  HISPANIC OR LATINO                 1              11
  NOT HISPANIC OR LATINO             3              33
[1] 2 2
[1] FALSE

Clustering(20) Variable = SGK1 MUTATION ANALYSIS
D20V1, survival
                sevent
clus2             0  1
  SGK1 MUTATED    3  1
  SGK1 WILD-TYPE 35  8
  SGK1 MUTATED SGK1 WILD-TYPE 
             4             43 
  SGK1 MUTATED SGK1 WILD-TYPE 
             1              8 
$`SGK1 MUTATED`
TCGA-FA-8693 TCGA-FF-8062 TCGA-G8-6909 TCGA-GR-7351 
        4.34        22.32       116.81       150.51 

$`SGK1 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-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-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       31.96        41.16        51.98        70.06       211.23        19.56 
TCGA-G8-6914 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      196.60        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 

  SGK1 MUTATED SGK1 WILD-TYPE 
          4.34           0.03 
  SGK1 MUTATED SGK1 WILD-TYPE 
        150.51         211.23 
  SGK1 MUTATED SGK1 WILD-TYPE 
        69.565         27.350 
[1] "4.3 - 150.5 (69.6)" "0.0 - 211.2 (27.4)"
[1] "hr=" "1"  
D20V2, continuous
                vv
clus             ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  SGK1 MUTATED         0                  0    0     0      0     0     0
  SGK1 WILD-TYPE       2                  2    4     3      1     2     1
                vv
clus             OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  SGK1 MUTATED                       0             0               0
  SGK1 WILD-TYPE                     1             1               3
                vv
clus             SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  SGK1 MUTATED                                               0       1       2
  SGK1 WILD-TYPE                                             1       1       0
D20V3, multiclass
                                               clus
vv                                              SGK1 MUTATED SGK1 WILD-TYPE
  ADRENAL                                                  0              2
  ASCITES/PERITONEUM                                       0              2
  BONE                                                     0              4
  BRAIN                                                    0              3
  BREAST                                                   0              1
  COLON                                                    0              2
  LIVER                                                    0              1
  OTHER EXTRANODAL SITE                                    0              1
  PAROTID GLAND                                            0              1
  SMALL INTESTINE                                          0              3
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)            0              1
  STOMACH                                                  1              1
  THYROID                                                  2              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V4, binary
                cls
clus              0  1
  SGK1 MUTATED    2  2
  SGK1 WILD-TYPE 24 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK1 MUTATED      2    2
  SGK1 WILD-TYPE   24   20
        clus
vv       SGK1 MUTATED SGK1 WILD-TYPE
  FEMALE            2             24
  MALE              2             20
[1] 2 2
[1] FALSE
D20V5, binary
                cls
clus              0  1
  SGK1 MUTATED    3  1
  SGK1 WILD-TYPE 37  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK1 MUTATED      3    1
  SGK1 WILD-TYPE   37    6
     clus
vv    SGK1 MUTATED SGK1 WILD-TYPE
  NO             3             37
  YES            1              6
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  SGK1 MUTATED                                                                                   4
  SGK1 WILD-TYPE                                                                                37
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  SGK1 MUTATED                          0                                  0
  SGK1 WILD-TYPE                        3                                  4
D20V6, multiclass
                                                                                   clus
vv                                                                                  SGK1 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                                                                                  SGK1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             37
  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
  SGK1 MUTATED       1                         0     3
  SGK1 WILD-TYPE    17                         1    26
D20V7, multiclass
                           clus
vv                          SGK1 MUTATED SGK1 WILD-TYPE
  ASIAN                                1             17
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                3             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, binary
                cls
clus              0  1
  SGK1 MUTATED    0  4
  SGK1 WILD-TYPE 12 32
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK1 MUTATED      0    4
  SGK1 WILD-TYPE   12   32
                        clus
vv                       SGK1 MUTATED SGK1 WILD-TYPE
  HISPANIC OR LATINO                0             12
  NOT HISPANIC OR LATINO            4             32
[1] 2 2
[1] FALSE

Clustering(21) Variable = IFITM3 MUTATION ANALYSIS
D21V1, survival
                  sevent
clus2               0  1
  IFITM3 MUTATED    2  1
  IFITM3 WILD-TYPE 36  8
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               3               44 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               1                8 
$`IFITM3 MUTATED`
TCGA-FF-8043 TCGA-FF-8046 TCGA-G8-6324 
       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-8041 TCGA-FF-8042 TCGA-FF-8047 
        8.15        14.04        18.18        35.54        31.10         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-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       31.96        51.98        70.06       211.23        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        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-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  IFITM3 MUTATED IFITM3 WILD-TYPE 
           24.69             0.03 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
           41.16           211.23 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
           31.73            26.68 
[1] "24.7 - 41.2 (31.7)" "0.0 - 211.2 (26.7)"
[1] "hr=" "2"  
D21V2, continuous
                  vv
clus               ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  IFITM3 MUTATED         0                  1    0     0      0     1     0
  IFITM3 WILD-TYPE       2                  1    4     3      1     1     1
                  vv
clus               OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  IFITM3 MUTATED                       0             0               0
  IFITM3 WILD-TYPE                     1             1               3
                  vv
clus               SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  IFITM3 MUTATED                                               0       0
  IFITM3 WILD-TYPE                                             1       2
                  vv
clus               THYROID
  IFITM3 MUTATED         0
  IFITM3 WILD-TYPE       2
D21V3, multiclass
[1] "Remove cluster labels:" "IFITM3 MUTATED"        
clus
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               2               23 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A4XK       TCGA-FA-A7DS 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
      TCGA-FA-A82F       TCGA-FF-8061       TCGA-FF-8062       TCGA-FF-A7CQ 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
      TCGA-FF-A7CR       TCGA-FF-A7CW       TCGA-FF-A7CX       TCGA-FM-8000 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
      TCGA-G8-6326       TCGA-G8-6906       TCGA-GR-7351       TCGA-GR-A4D4 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
      TCGA-GR-A4D5       TCGA-GR-A4D9       TCGA-GS-A9TT       TCGA-RQ-A68N 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
      TCGA-RQ-A6JB       TCGA-RQ-AAAT       TCGA-VB-A8QN 
"IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" "IFITM3 WILD-TYPE" 
D21V4, binary
                  cls
clus                0  1
  IFITM3 MUTATED    2  1
  IFITM3 WILD-TYPE 24 21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      2    1
  IFITM3 WILD-TYPE   24   21
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  FEMALE              2               24
  MALE                1               21
[1] 2 2
[1] FALSE
D21V5, binary
                  cls
clus                0  1
  IFITM3 MUTATED    3  0
  IFITM3 WILD-TYPE 37  7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      3    0
  IFITM3 WILD-TYPE   37    7
     clus
vv    IFITM3 MUTATED IFITM3 WILD-TYPE
  NO               3               37
  YES              0                7
[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                                                                                38
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  IFITM3 MUTATED                          0                                  0
  IFITM3 WILD-TYPE                        3                                  4
D21V6, 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                                                             0
                                                                                   clus
vv                                                                                  IFITM3 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               38
  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
  IFITM3 MUTATED       2                         1     0
  IFITM3 WILD-TYPE    16                         0    29
D21V7, multiclass
                           clus
vv                          IFITM3 MUTATED IFITM3 WILD-TYPE
  ASIAN                                  2               16
  BLACK OR AFRICAN AMERICAN              1                0
  WHITE                                  0               29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, binary
                  cls
clus                0  1
  IFITM3 MUTATED    0  3
  IFITM3 WILD-TYPE 12 33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      0    3
  IFITM3 WILD-TYPE   12   33
                        clus
vv                       IFITM3 MUTATED IFITM3 WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              3               33
[1] 2 2
[1] FALSE

Clustering(22) Variable = APOB MUTATION ANALYSIS
D22V1, survival
                sevent
clus2             0  1
  APOB MUTATED    2  1
  APOB WILD-TYPE 36  8
  APOB MUTATED APOB WILD-TYPE 
             3             44 
  APOB MUTATED APOB WILD-TYPE 
             1              8 
$`APOB MUTATED`
TCGA-G8-6324 TCGA-G8-6914 TCGA-GS-A9TW 
       41.16       196.60        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-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       26.01        12.66        31.96        51.98        70.06       211.23 
TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
       19.56       116.81       150.51        98.07        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-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 

  APOB MUTATED APOB WILD-TYPE 
         41.16           0.03 
  APOB MUTATED APOB WILD-TYPE 
        196.60         211.23 
  APOB MUTATED APOB WILD-TYPE 
         53.16          25.96 
[1] "41.2 - 196.6 (53.2)" "0.0 - 211.2 (26.0)" 
[1] "hr=" "1.2"
D22V2, continuous
                vv
clus             ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  APOB MUTATED         0                  1    0     0      0     0     0
  APOB WILD-TYPE       2                  1    4     3      1     2     1
                vv
clus             OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  APOB MUTATED                       0             0               0
  APOB WILD-TYPE                     1             1               3
                vv
clus             SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  APOB MUTATED                                               0       0       0
  APOB WILD-TYPE                                             1       2       2
D22V3, multiclass
[1] "Remove cluster labels:" "APOB MUTATED"          
clus
  APOB MUTATED APOB WILD-TYPE 
             1             24 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A7DS 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-FA-A82F     TCGA-FF-8043     TCGA-FF-8061     TCGA-FF-8062 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-FF-A7CQ     TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-FM-8000     TCGA-G8-6326     TCGA-G8-6906     TCGA-GR-7351 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-GR-A4D4     TCGA-GR-A4D5     TCGA-GR-A4D9     TCGA-GS-A9TT 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-A6JB     TCGA-RQ-AAAT     TCGA-VB-A8QN 
"APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" "APOB WILD-TYPE" 
D22V4, binary
                cls
clus              0  1
  APOB MUTATED    2  1
  APOB WILD-TYPE 24 21
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED      2    1
  APOB WILD-TYPE   24   21
        clus
vv       APOB MUTATED APOB WILD-TYPE
  FEMALE            2             24
  MALE              1             21
[1] 2 2
[1] FALSE
D22V5, binary
                cls
clus              0  1
  APOB MUTATED    2  1
  APOB WILD-TYPE 38  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED      2    1
  APOB WILD-TYPE   38    6
     clus
vv    APOB MUTATED APOB WILD-TYPE
  NO             2             38
  YES            1              6
[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                                                                                39
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  APOB MUTATED                          0                                  1
  APOB WILD-TYPE                        3                                  3
D22V6, 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)             39
  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    27
D22V7, multiclass
                           clus
vv                          APOB MUTATED APOB WILD-TYPE
  ASIAN                                0             18
  BLACK OR AFRICAN AMERICAN            1              0
  WHITE                                2             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, binary
                cls
clus              0  1
  APOB MUTATED    1  2
  APOB WILD-TYPE 11 34
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED      1    2
  APOB WILD-TYPE   11   34
                        clus
vv                       APOB MUTATED APOB WILD-TYPE
  HISPANIC OR LATINO                1             11
  NOT HISPANIC OR LATINO            2             34
[1] 2 2
[1] FALSE

Clustering(23) Variable = MCM8 MUTATION ANALYSIS
D23V1, survival
                sevent
clus2             0  1
  MCM8 MUTATED    1  2
  MCM8 WILD-TYPE 37  7
  MCM8 MUTATED MCM8 WILD-TYPE 
             3             44 
  MCM8 MUTATED MCM8 WILD-TYPE 
             2              7 
$`MCM8 MUTATED`
TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 
       41.16        70.06       211.23 

$`MCM8 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-G8-6325 TCGA-G8-6907 TCGA-G8-6909 
       26.01        12.66        31.96        51.98        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        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-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  MCM8 MUTATED MCM8 WILD-TYPE 
         41.16           0.03 
  MCM8 MUTATED MCM8 WILD-TYPE 
        211.23         196.60 
  MCM8 MUTATED MCM8 WILD-TYPE 
         70.06          25.96 
[1] "41.2 - 211.2 (70.1)" "0.0 - 196.6 (26.0)" 
[1] "hr=" "1.2"
D23V2, continuous
                vv
clus             ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  MCM8 MUTATED         0                  2    0     0      0     0     0
  MCM8 WILD-TYPE       2                  0    4     3      1     2     1
                vv
clus             OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  MCM8 MUTATED                       1             0               0
  MCM8 WILD-TYPE                     0             1               3
                vv
clus             SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  MCM8 MUTATED                                               0       0       0
  MCM8 WILD-TYPE                                             1       2       2
D23V3, multiclass
                                               clus
vv                                              MCM8 MUTATED MCM8 WILD-TYPE
  ADRENAL                                                  0              2
  ASCITES/PERITONEUM                                       2              0
  BONE                                                     0              4
  BRAIN                                                    0              3
  BREAST                                                   0              1
  COLON                                                    0              2
  LIVER                                                    0              1
  OTHER EXTRANODAL SITE                                    1              0
  PAROTID GLAND                                            0              1
  SMALL INTESTINE                                          0              3
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)            0              1
  STOMACH                                                  0              2
  THYROID                                                  0              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V4, binary
                cls
clus              0  1
  MCM8 MUTATED    1  2
  MCM8 WILD-TYPE 25 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM8 MUTATED      1    2
  MCM8 WILD-TYPE   25   20
        clus
vv       MCM8 MUTATED MCM8 WILD-TYPE
  FEMALE            1             25
  MALE              2             20
[1] 2 2
[1] FALSE
D23V5, binary
                cls
clus              0  1
  MCM8 MUTATED    3  0
  MCM8 WILD-TYPE 37  7
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM8 MUTATED      3    0
  MCM8 WILD-TYPE   37    7
     clus
vv    MCM8 MUTATED MCM8 WILD-TYPE
  NO             3             37
  YES            0              7
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  MCM8 MUTATED                                                                                   3
  MCM8 WILD-TYPE                                                                                38
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  MCM8 MUTATED                          0                                  0
  MCM8 WILD-TYPE                        3                                  4
D23V6, multiclass
                                                                                   clus
vv                                                                                  MCM8 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                                                                                  MCM8 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             38
  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
  MCM8 MUTATED       0                         1     2
  MCM8 WILD-TYPE    18                         0    27
D23V7, multiclass
                           clus
vv                          MCM8 MUTATED MCM8 WILD-TYPE
  ASIAN                                0             18
  BLACK OR AFRICAN AMERICAN            1              0
  WHITE                                2             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
                cls
clus              0  1
  MCM8 MUTATED    0  3
  MCM8 WILD-TYPE 12 33
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM8 MUTATED      0    3
  MCM8 WILD-TYPE   12   33
                        clus
vv                       MCM8 MUTATED MCM8 WILD-TYPE
  HISPANIC OR LATINO                0             12
  NOT HISPANIC OR LATINO            3             33
[1] 2 2
[1] FALSE

Clustering(24) Variable = ARID1A MUTATION ANALYSIS
D24V1, survival
                  sevent
clus2               0  1
  ARID1A MUTATED    4  1
  ARID1A WILD-TYPE 34  8
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               42 
  ARID1A MUTATED ARID1A WILD-TYPE 
               1                8 
$`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-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       12.66        51.98        70.06       211.23        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GS-A9TQ 
      196.60       150.51        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 

  ARID1A MUTATED ARID1A WILD-TYPE 
           18.18             0.03 
  ARID1A MUTATED ARID1A WILD-TYPE 
           57.17           211.23 
  ARID1A MUTATED ARID1A WILD-TYPE 
           41.16            25.96 
[1] "18.2 - 57.2 (41.2)" "0.0 - 211.2 (26.0)"
[1] "hr=" "1.1"
D24V2, continuous
                  vv
clus               ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  ARID1A MUTATED         0                  1    1     0      0     1     0
  ARID1A WILD-TYPE       2                  1    3     3      1     1     1
                  vv
clus               OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  ARID1A MUTATED                       0             0               0
  ARID1A WILD-TYPE                     1             1               3
                  vv
clus               SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  ARID1A MUTATED                                               1       0
  ARID1A WILD-TYPE                                             0       2
                  vv
clus               THYROID
  ARID1A MUTATED         0
  ARID1A WILD-TYPE       2
D24V3, multiclass
                                               clus
vv                                              ARID1A MUTATED ARID1A WILD-TYPE
  ADRENAL                                                    0                2
  ASCITES/PERITONEUM                                         1                1
  BONE                                                       1                3
  BRAIN                                                      0                3
  BREAST                                                     0                1
  COLON                                                      1                1
  LIVER                                                      0                1
  OTHER EXTRANODAL SITE                                      0                1
  PAROTID GLAND                                              0                1
  SMALL INTESTINE                                            0                3
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)              1                0
  STOMACH                                                    0                2
  THYROID                                                    0                2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V4, binary
                  cls
clus                0  1
  ARID1A MUTATED    5  0
  ARID1A WILD-TYPE 21 22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      5    0
  ARID1A WILD-TYPE   21   22
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              5               21
  MALE                0               22
[1] 2 2
[1] FALSE
D24V5, binary
                  cls
clus                0  1
  ARID1A MUTATED    5  0
  ARID1A WILD-TYPE 35  7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      5    0
  ARID1A WILD-TYPE   35    7
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO               5               35
  YES              0                7
[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                                                                                36
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  ARID1A MUTATED                          0                                  0
  ARID1A WILD-TYPE                        3                                  4
D24V6, 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)               36
  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    25
D24V7, multiclass
                           clus
vv                          ARID1A MUTATED ARID1A WILD-TYPE
  ASIAN                                  0               18
  BLACK OR AFRICAN AMERICAN              1                0
  WHITE                                  4               25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                  cls
clus                0  1
  ARID1A MUTATED    0  5
  ARID1A WILD-TYPE 12 31
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      0    5
  ARID1A WILD-TYPE   12   31
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              5               31
[1] 2 2
[1] FALSE

Clustering(25) Variable = PCDHA10 MUTATION ANALYSIS
D25V1, survival
                   sevent
clus2                0  1
  PCDHA10 MUTATED    4  2
  PCDHA10 WILD-TYPE 34  7
  PCDHA10 MUTATED PCDHA10 WILD-TYPE 
                6                41 
  PCDHA10 MUTATED PCDHA10 WILD-TYPE 
                2                 7 
$`PCDHA10 MUTATED`
TCGA-FF-8061 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7353 TCGA-GS-A9U3 
       27.35        19.56       116.81       196.60        98.07       111.58 

$`PCDHA10 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-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       12.66        31.96        41.16        51.98        70.06       211.23 
TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
      150.51        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-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15        12.85        25.91         0.03         0.56 

  PCDHA10 MUTATED PCDHA10 WILD-TYPE 
            19.56              0.03 
  PCDHA10 MUTATED PCDHA10 WILD-TYPE 
           196.60            211.23 
  PCDHA10 MUTATED PCDHA10 WILD-TYPE 
          104.825            25.910 
[1] "19.6 - 196.6 (104.8)" "0.0 - 211.2 (25.9)"  
[1] "hr=" "1.4"
D25V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  PCDHA10 MUTATED         0                  0    0     0      0     0     0
  PCDHA10 WILD-TYPE       2                  2    4     3      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  PCDHA10 MUTATED                       0             0               1
  PCDHA10 WILD-TYPE                     1             1               2
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  PCDHA10 MUTATED                                               0       0
  PCDHA10 WILD-TYPE                                             1       2
                   vv
clus                THYROID
  PCDHA10 MUTATED         0
  PCDHA10 WILD-TYPE       2
D25V3, multiclass
[1] "Remove cluster labels:" "PCDHA10 MUTATED"       
clus
  PCDHA10 MUTATED PCDHA10 WILD-TYPE 
                1                24 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A7DS 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
       TCGA-FA-A82F        TCGA-FF-8043        TCGA-FF-8062        TCGA-FF-A7CQ 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
       TCGA-FF-A7CR        TCGA-FF-A7CW        TCGA-FF-A7CX        TCGA-FM-8000 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6326        TCGA-G8-6906        TCGA-GR-7351 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
       TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D9        TCGA-GS-A9TT 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-RQ-AAAT        TCGA-VB-A8QN 
"PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" "PCDHA10 WILD-TYPE" 
D25V4, binary
                   cls
clus                 0  1
  PCDHA10 MUTATED    2  4
  PCDHA10 WILD-TYPE 24 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHA10 MUTATED      2    4
  PCDHA10 WILD-TYPE   24   18
        clus
vv       PCDHA10 MUTATED PCDHA10 WILD-TYPE
  FEMALE               2                24
  MALE                 4                18
[1] 2 2
[1] FALSE
D25V5, binary
                   cls
clus                 0  1
  PCDHA10 MUTATED    6  0
  PCDHA10 WILD-TYPE 34  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHA10 MUTATED      6    0
  PCDHA10 WILD-TYPE   34    7
     clus
vv    PCDHA10 MUTATED PCDHA10 WILD-TYPE
  NO                6                34
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  PCDHA10 MUTATED                                                                                   6
  PCDHA10 WILD-TYPE                                                                                35
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  PCDHA10 MUTATED                          0                                  0
  PCDHA10 WILD-TYPE                        3                                  4
D25V6, multiclass
                                                                                   clus
vv                                                                                  PCDHA10 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                                                                                  PCDHA10 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                35
  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
  PCDHA10 MUTATED       1                         0     5
  PCDHA10 WILD-TYPE    17                         1    24
D25V7, multiclass
                           clus
vv                          PCDHA10 MUTATED PCDHA10 WILD-TYPE
  ASIAN                                   1                17
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   5                24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, binary
                   cls
clus                 0  1
  PCDHA10 MUTATED    1  5
  PCDHA10 WILD-TYPE 11 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHA10 MUTATED      1    5
  PCDHA10 WILD-TYPE   11   31
                        clus
vv                       PCDHA10 MUTATED PCDHA10 WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               5                31
[1] 2 2
[1] FALSE

Clustering(26) Variable = LRRC16B MUTATION ANALYSIS
D26V1, survival
                   sevent
clus2                0  1
  LRRC16B MUTATED    3  1
  LRRC16B WILD-TYPE 35  8
  LRRC16B MUTATED LRRC16B WILD-TYPE 
                4                43 
  LRRC16B MUTATED LRRC16B WILD-TYPE 
                1                 8 
$`LRRC16B MUTATED`
TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 
       19.56       196.60       150.51        98.07 

$`LRRC16B 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-G8-6325 TCGA-G8-6326 
       26.01        12.66        31.96        41.16        51.98        70.06 
TCGA-G8-6906 TCGA-G8-6909 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      211.23       116.81        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 

  LRRC16B MUTATED LRRC16B WILD-TYPE 
            19.56              0.03 
  LRRC16B MUTATED LRRC16B WILD-TYPE 
           196.60            211.23 
  LRRC16B MUTATED LRRC16B WILD-TYPE 
           124.29             26.01 
[1] "19.6 - 196.6 (124.3)" "0.0 - 211.2 (26.0)"  
[1] "hr=" "1.2"
D26V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  LRRC16B MUTATED         0                  0    0     0      0     0     0
  LRRC16B WILD-TYPE       2                  2    4     3      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  LRRC16B MUTATED                       0             0               0
  LRRC16B WILD-TYPE                     1             1               3
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  LRRC16B MUTATED                                               0       0
  LRRC16B WILD-TYPE                                             1       2
                   vv
clus                THYROID
  LRRC16B MUTATED         1
  LRRC16B WILD-TYPE       1
D26V3, multiclass
[1] "Remove cluster labels:" "LRRC16B MUTATED"       
clus
  LRRC16B MUTATED LRRC16B WILD-TYPE 
                1                24 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A7DS 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
       TCGA-FA-A82F        TCGA-FF-8043        TCGA-FF-8061        TCGA-FF-8062 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
       TCGA-FF-A7CQ        TCGA-FF-A7CR        TCGA-FF-A7CW        TCGA-FF-A7CX 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
       TCGA-FM-8000        TCGA-G8-6324        TCGA-G8-6326        TCGA-G8-6906 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
       TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D9        TCGA-GS-A9TT 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-RQ-AAAT        TCGA-VB-A8QN 
"LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" "LRRC16B WILD-TYPE" 
D26V4, binary
                   cls
clus                 0  1
  LRRC16B MUTATED    2  2
  LRRC16B WILD-TYPE 24 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRC16B MUTATED      2    2
  LRRC16B WILD-TYPE   24   20
        clus
vv       LRRC16B MUTATED LRRC16B WILD-TYPE
  FEMALE               2                24
  MALE                 2                20
[1] 2 2
[1] FALSE
D26V5, binary
                   cls
clus                 0  1
  LRRC16B MUTATED    3  1
  LRRC16B WILD-TYPE 37  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRC16B MUTATED      3    1
  LRRC16B WILD-TYPE   37    6
     clus
vv    LRRC16B MUTATED LRRC16B WILD-TYPE
  NO                3                37
  YES               1                 6
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  LRRC16B MUTATED                                                                                   4
  LRRC16B WILD-TYPE                                                                                37
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  LRRC16B MUTATED                          0                                  0
  LRRC16B WILD-TYPE                        3                                  4
D26V6, multiclass
                                                                                   clus
vv                                                                                  LRRC16B 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                                                                                  LRRC16B WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                37
  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
  LRRC16B MUTATED       0                         0     4
  LRRC16B WILD-TYPE    18                         1    25
D26V7, multiclass
                           clus
vv                          LRRC16B MUTATED LRRC16B WILD-TYPE
  ASIAN                                   0                18
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   4                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, binary
                   cls
clus                 0  1
  LRRC16B MUTATED    0  4
  LRRC16B WILD-TYPE 12 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRC16B MUTATED      0    4
  LRRC16B WILD-TYPE   12   32
                        clus
vv                       LRRC16B MUTATED LRRC16B WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               4                32
[1] 2 2
[1] FALSE

Clustering(27) Variable = PNPLA7 MUTATION ANALYSIS
D27V1, survival
                  sevent
clus2               0  1
  PNPLA7 MUTATED    2  1
  PNPLA7 WILD-TYPE 36  8
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
               3               44 
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
               1                8 
$`PNPLA7 MUTATED`
TCGA-G8-6325 TCGA-G8-6906 TCGA-G8-6914 
       51.98       211.23       196.60 

$`PNPLA7 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-G8-6326 TCGA-G8-6907 
       26.01        12.66        31.96        41.16        70.06        19.56 
TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      116.81       150.51        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-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
           51.98             0.03 
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
          211.23           150.51 
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
          196.60            25.96 
[1] "52.0 - 211.2 (196.6)" "0.0 - 150.5 (26.0)"  
[1] "hr="   "1e+08"
D27V2, continuous
                  vv
clus               ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  PNPLA7 MUTATED         0                  0    0     0      0     0     0
  PNPLA7 WILD-TYPE       2                  2    4     3      1     2     1
                  vv
clus               OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  PNPLA7 MUTATED                       1             0               0
  PNPLA7 WILD-TYPE                     0             1               3
                  vv
clus               SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  PNPLA7 MUTATED                                               0       0
  PNPLA7 WILD-TYPE                                             1       2
                  vv
clus               THYROID
  PNPLA7 MUTATED         0
  PNPLA7 WILD-TYPE       2
D27V3, multiclass
[1] "Remove cluster labels:" "PNPLA7 MUTATED"        
clus
  PNPLA7 MUTATED PNPLA7 WILD-TYPE 
               1               24 
      TCGA-FA-8693       TCGA-FA-A4BB       TCGA-FA-A4XK       TCGA-FA-A7DS 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-FA-A82F       TCGA-FF-8043       TCGA-FF-8061       TCGA-FF-8062 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-FF-A7CQ       TCGA-FF-A7CR       TCGA-FF-A7CW       TCGA-FF-A7CX 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-FM-8000       TCGA-G8-6324       TCGA-G8-6326       TCGA-GR-7351 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-GR-A4D4       TCGA-GR-A4D5       TCGA-GR-A4D9       TCGA-GS-A9TT 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
      TCGA-RQ-A68N       TCGA-RQ-A6JB       TCGA-RQ-AAAT       TCGA-VB-A8QN 
"PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" "PNPLA7 WILD-TYPE" 
D27V4, binary
                  cls
clus                0  1
  PNPLA7 MUTATED    0  3
  PNPLA7 WILD-TYPE 26 19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA7 MUTATED      0    3
  PNPLA7 WILD-TYPE   26   19
        clus
vv       PNPLA7 MUTATED PNPLA7 WILD-TYPE
  FEMALE              0               26
  MALE                3               19
[1] 2 2
[1] FALSE
D27V5, binary
                  cls
clus                0  1
  PNPLA7 MUTATED    3  0
  PNPLA7 WILD-TYPE 37  7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA7 MUTATED      3    0
  PNPLA7 WILD-TYPE   37    7
     clus
vv    PNPLA7 MUTATED PNPLA7 WILD-TYPE
  NO               3               37
  YES              0                7
[1] 2 2
[1] FALSE
                  vv
clus               DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  PNPLA7 MUTATED                                                                                   3
  PNPLA7 WILD-TYPE                                                                                38
                  vv
clus               PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  PNPLA7 MUTATED                          0                                  0
  PNPLA7 WILD-TYPE                        3                                  4
D27V6, multiclass
                                                                                   clus
vv                                                                                  PNPLA7 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                                                                                  PNPLA7 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               38
  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
  PNPLA7 MUTATED       0                         0     3
  PNPLA7 WILD-TYPE    18                         1    26
D27V7, multiclass
                           clus
vv                          PNPLA7 MUTATED PNPLA7 WILD-TYPE
  ASIAN                                  0               18
  BLACK OR AFRICAN AMERICAN              0                1
  WHITE                                  3               26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                  cls
clus                0  1
  PNPLA7 MUTATED    0  3
  PNPLA7 WILD-TYPE 12 33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA7 MUTATED      0    3
  PNPLA7 WILD-TYPE   12   33
                        clus
vv                       PNPLA7 MUTATED PNPLA7 WILD-TYPE
  HISPANIC OR LATINO                  0               12
  NOT HISPANIC OR LATINO              3               33
[1] 2 2
[1] FALSE

Clustering(28) Variable = SLC16A8 MUTATION ANALYSIS
D28V1, survival
                   sevent
clus2                0  1
  SLC16A8 MUTATED    2  1
  SLC16A8 WILD-TYPE 36  8
  SLC16A8 MUTATED SLC16A8 WILD-TYPE 
                3                44 
  SLC16A8 MUTATED SLC16A8 WILD-TYPE 
                1                 8 
$`SLC16A8 MUTATED`
TCGA-G8-6325 TCGA-G8-6907 TCGA-GR-7353 
       51.98        19.56        98.07 

$`SLC16A8 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-G8-6326 TCGA-G8-6906 
       26.01        12.66        31.96        41.16        70.06       211.23 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      116.81       196.60       150.51        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-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  SLC16A8 MUTATED SLC16A8 WILD-TYPE 
            19.56              0.03 
  SLC16A8 MUTATED SLC16A8 WILD-TYPE 
            98.07            211.23 
  SLC16A8 MUTATED SLC16A8 WILD-TYPE 
            51.98             26.68 
[1] "19.6 - 98.1 (52.0)" "0.0 - 211.2 (26.7)"
[1] "hr=" "1.9"
D28V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  SLC16A8 MUTATED         0                  0    0     0      0     0     0
  SLC16A8 WILD-TYPE       2                  2    4     3      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  SLC16A8 MUTATED                       0             0               0
  SLC16A8 WILD-TYPE                     1             1               3
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  SLC16A8 MUTATED                                               0       0
  SLC16A8 WILD-TYPE                                             1       2
                   vv
clus                THYROID
  SLC16A8 MUTATED         0
  SLC16A8 WILD-TYPE       2
D28V3, multiclass
D28V4, binary
                   cls
clus                 0  1
  SLC16A8 MUTATED    1  2
  SLC16A8 WILD-TYPE 25 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A8 MUTATED      1    2
  SLC16A8 WILD-TYPE   25   20
        clus
vv       SLC16A8 MUTATED SLC16A8 WILD-TYPE
  FEMALE               1                25
  MALE                 2                20
[1] 2 2
[1] FALSE
D28V5, binary
                   cls
clus                 0  1
  SLC16A8 MUTATED    3  0
  SLC16A8 WILD-TYPE 37  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A8 MUTATED      3    0
  SLC16A8 WILD-TYPE   37    7
     clus
vv    SLC16A8 MUTATED SLC16A8 WILD-TYPE
  NO                3                37
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  SLC16A8 MUTATED                                                                                   3
  SLC16A8 WILD-TYPE                                                                                38
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  SLC16A8 MUTATED                          0                                  0
  SLC16A8 WILD-TYPE                        3                                  4
D28V6, multiclass
                                                                                   clus
vv                                                                                  SLC16A8 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                                                                                  SLC16A8 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                38
  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
  SLC16A8 MUTATED       0                         0     3
  SLC16A8 WILD-TYPE    18                         1    26
D28V7, multiclass
                           clus
vv                          SLC16A8 MUTATED SLC16A8 WILD-TYPE
  ASIAN                                   0                18
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, binary
                   cls
clus                 0  1
  SLC16A8 MUTATED    0  3
  SLC16A8 WILD-TYPE 12 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A8 MUTATED      0    3
  SLC16A8 WILD-TYPE   12   33
                        clus
vv                       SLC16A8 MUTATED SLC16A8 WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               3                33
[1] 2 2
[1] FALSE

Clustering(29) Variable = PKHD1L1 MUTATION ANALYSIS
D29V1, survival
                   sevent
clus2                0  1
  PKHD1L1 MUTATED    3  2
  PKHD1L1 WILD-TYPE 35  7
  PKHD1L1 MUTATED PKHD1L1 WILD-TYPE 
                5                42 
  PKHD1L1 MUTATED PKHD1L1 WILD-TYPE 
                2                 7 
$`PKHD1L1 MUTATED`
TCGA-FF-8041 TCGA-G8-6324 TCGA-G8-6907 TCGA-GR-7353 TCGA-GS-A9TZ 
       35.54        41.16        19.56        98.07        25.15 

$`PKHD1L1 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-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-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 
       12.66        31.96        51.98        70.06       211.23       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      196.60       150.51        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-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
      109.58       111.58        12.85        25.91         0.03         0.56 

  PKHD1L1 MUTATED PKHD1L1 WILD-TYPE 
            19.56              0.03 
  PKHD1L1 MUTATED PKHD1L1 WILD-TYPE 
            98.07            211.23 
  PKHD1L1 MUTATED PKHD1L1 WILD-TYPE 
            35.54             26.68 
[1] "19.6 - 98.1 (35.5)" "0.0 - 211.2 (26.7)"
[1] "hr=" "2.8"
D29V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  PKHD1L1 MUTATED         0                  1    0     0      0     0     0
  PKHD1L1 WILD-TYPE       2                  1    4     3      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  PKHD1L1 MUTATED                       0             0               0
  PKHD1L1 WILD-TYPE                     1             1               3
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  PKHD1L1 MUTATED                                               0       0
  PKHD1L1 WILD-TYPE                                             1       2
                   vv
clus                THYROID
  PKHD1L1 MUTATED         0
  PKHD1L1 WILD-TYPE       2
D29V3, multiclass
[1] "Remove cluster labels:" "PKHD1L1 MUTATED"       
clus
  PKHD1L1 MUTATED PKHD1L1 WILD-TYPE 
                1                24 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A7DS 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
       TCGA-FA-A82F        TCGA-FF-8043        TCGA-FF-8061        TCGA-FF-8062 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
       TCGA-FF-A7CQ        TCGA-FF-A7CR        TCGA-FF-A7CW        TCGA-FF-A7CX 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
       TCGA-FM-8000        TCGA-G8-6326        TCGA-G8-6906        TCGA-GR-7351 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
       TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D9        TCGA-GS-A9TT 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-RQ-AAAT        TCGA-VB-A8QN 
"PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" "PKHD1L1 WILD-TYPE" 
D29V4, binary
                   cls
clus                 0  1
  PKHD1L1 MUTATED    3  2
  PKHD1L1 WILD-TYPE 23 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PKHD1L1 MUTATED      3    2
  PKHD1L1 WILD-TYPE   23   20
        clus
vv       PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  FEMALE               3                23
  MALE                 2                20
[1] 2 2
[1] FALSE
D29V5, binary
                   cls
clus                 0  1
  PKHD1L1 MUTATED    4  1
  PKHD1L1 WILD-TYPE 36  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PKHD1L1 MUTATED      4    1
  PKHD1L1 WILD-TYPE   36    6
     clus
vv    PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  NO                4                36
  YES               1                 6
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  PKHD1L1 MUTATED                                                                                   3
  PKHD1L1 WILD-TYPE                                                                                38
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  PKHD1L1 MUTATED                          0                                  2
  PKHD1L1 WILD-TYPE                        3                                  2
D29V6, multiclass
                                                                                   clus
vv                                                                                  PKHD1L1 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                                                                                  PKHD1L1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                38
  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
  PKHD1L1 MUTATED       1                         1     3
  PKHD1L1 WILD-TYPE    17                         0    26
D29V7, multiclass
                           clus
vv                          PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  ASIAN                                   1                17
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                   3                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V8, binary
                   cls
clus                 0  1
  PKHD1L1 MUTATED    1  4
  PKHD1L1 WILD-TYPE 11 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PKHD1L1 MUTATED      1    4
  PKHD1L1 WILD-TYPE   11   32
                        clus
vv                       PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               4                32
[1] 2 2
[1] FALSE

Clustering(30) Variable = HRCT1 MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2              0  1
  HRCT1 MUTATED    2  2
  HRCT1 WILD-TYPE 36  7
  HRCT1 MUTATED HRCT1 WILD-TYPE 
              4              43 
  HRCT1 MUTATED HRCT1 WILD-TYPE 
              2               7 
$`HRCT1 MUTATED`
TCGA-FF-8046 TCGA-FF-8061 TCGA-G8-6324 TCGA-G8-6906 
       24.69        27.35        41.16       211.23 

$`HRCT1 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-8047 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
        4.14        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       31.96        51.98        70.06        19.56       116.81       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      150.51        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 

  HRCT1 MUTATED HRCT1 WILD-TYPE 
          24.69            0.03 
  HRCT1 MUTATED HRCT1 WILD-TYPE 
         211.23          196.60 
  HRCT1 MUTATED HRCT1 WILD-TYPE 
         34.255          26.010 
[1] "24.7 - 211.2 (34.3)" "0.0 - 196.6 (26.0)" 
[1] "hr=" "1.1"
D30V2, continuous
                 vv
clus              ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  HRCT1 MUTATED         0                  1    0     0      0     0     0
  HRCT1 WILD-TYPE       2                  1    4     3      1     2     1
                 vv
clus              OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  HRCT1 MUTATED                       1             0               1
  HRCT1 WILD-TYPE                     0             1               2
                 vv
clus              SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  HRCT1 MUTATED                                               0       0       0
  HRCT1 WILD-TYPE                                             1       2       2
D30V3, multiclass
                                               clus
vv                                              HRCT1 MUTATED HRCT1 WILD-TYPE
  ADRENAL                                                   0               2
  ASCITES/PERITONEUM                                        1               1
  BONE                                                      0               4
  BRAIN                                                     0               3
  BREAST                                                    0               1
  COLON                                                     0               2
  LIVER                                                     0               1
  OTHER EXTRANODAL SITE                                     1               0
  PAROTID GLAND                                             0               1
  SMALL INTESTINE                                           1               2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)             0               1
  STOMACH                                                   0               2
  THYROID                                                   0               2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V4, binary
                 cls
clus               0  1
  HRCT1 MUTATED    1  3
  HRCT1 WILD-TYPE 25 19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HRCT1 MUTATED      1    3
  HRCT1 WILD-TYPE   25   19
        clus
vv       HRCT1 MUTATED HRCT1 WILD-TYPE
  FEMALE             1              25
  MALE               3              19
[1] 2 2
[1] FALSE
D30V5, binary
                 cls
clus               0  1
  HRCT1 MUTATED    4  0
  HRCT1 WILD-TYPE 36  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HRCT1 MUTATED      4    0
  HRCT1 WILD-TYPE   36    7
     clus
vv    HRCT1 MUTATED HRCT1 WILD-TYPE
  NO              4              36
  YES             0               7
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  HRCT1 MUTATED                                                                                   4
  HRCT1 WILD-TYPE                                                                                37
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  HRCT1 MUTATED                          0                                  0
  HRCT1 WILD-TYPE                        3                                  4
D30V6, multiclass
                                                                                   clus
vv                                                                                  HRCT1 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                                                                                  HRCT1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              37
  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
  HRCT1 MUTATED       2                         1     1
  HRCT1 WILD-TYPE    16                         0    28
D30V7, multiclass
                           clus
vv                          HRCT1 MUTATED HRCT1 WILD-TYPE
  ASIAN                                 2              16
  BLACK OR AFRICAN AMERICAN             1               0
  WHITE                                 1              28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, binary
                 cls
clus               0  1
  HRCT1 MUTATED    0  4
  HRCT1 WILD-TYPE 12 32
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HRCT1 MUTATED      0    4
  HRCT1 WILD-TYPE   12   32
                        clus
vv                       HRCT1 MUTATED HRCT1 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             4              32
[1] 2 2
[1] FALSE

Clustering(31) Variable = TYRO3 MUTATION ANALYSIS
D31V1, survival
                 sevent
clus2              0  1
  TYRO3 MUTATED    3  1
  TYRO3 WILD-TYPE 35  8
  TYRO3 MUTATED TYRO3 WILD-TYPE 
              4              43 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
              1               8 
$`TYRO3 MUTATED`
TCGA-FF-A7CX TCGA-G8-6325 TCGA-G8-6906 TCGA-G8-6914 
       12.66        51.98       211.23       196.60 

$`TYRO3 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-G8-6324 TCGA-G8-6326 TCGA-G8-6907 TCGA-G8-6909 
       26.01        31.96        41.16        70.06        19.56       116.81 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      150.51        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 

  TYRO3 MUTATED TYRO3 WILD-TYPE 
          12.66            0.03 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
         211.23          150.51 
  TYRO3 MUTATED TYRO3 WILD-TYPE 
         124.29           26.01 
[1] "12.7 - 211.2 (124.3)" "0.0 - 150.5 (26.0)"  
[1] "hr="     "2.7e+08"
D31V2, continuous
                 vv
clus              ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  TYRO3 MUTATED         1                  0    0     0      0     0     0
  TYRO3 WILD-TYPE       1                  2    4     3      1     2     1
                 vv
clus              OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  TYRO3 MUTATED                       1             0               0
  TYRO3 WILD-TYPE                     0             1               3
                 vv
clus              SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  TYRO3 MUTATED                                               0       0       0
  TYRO3 WILD-TYPE                                             1       2       2
D31V3, multiclass
[1] "Remove cluster labels:" "TYRO3 MUTATED"         
clus
  TYRO3 MUTATED TYRO3 WILD-TYPE 
              2              23 
     TCGA-FA-8693      TCGA-FA-A4BB      TCGA-FA-A4XK      TCGA-FA-A7DS 
"TYRO3 WILD-TYPE" "TYRO3 WILD-TYPE" "TYRO3 WILD-TYPE" "TYRO3 WILD-TYPE" 
     TCGA-FA-A82F      TCGA-FF-8043      TCGA-FF-8061      TCGA-FF-8062 
"TYRO3 WILD-TYPE" "TYRO3 WILD-TYPE" "TYRO3 WILD-TYPE" "TYRO3 WILD-TYPE" 
     TCGA-FF-A7CQ      TCGA-FF-A7CR      TCGA-FF-A7CW      TCGA-FM-8000 
"TYRO3 WILD-TYPE" "TYRO3 WILD-TYPE" "TYRO3 WILD-TYPE" "TYRO3 WILD-TYPE" 
     TCGA-G8-6324      TCGA-G8-6326      TCGA-GR-7351      TCGA-GR-A4D4 
"TYRO3 WILD-TYPE" "TYRO3 WILD-TYPE" "TYRO3 WILD-TYPE" "TYRO3 WILD-TYPE" 
     TCGA-GR-A4D5      TCGA-GR-A4D9      TCGA-GS-A9TT      TCGA-RQ-A68N 
"TYRO3 WILD-TYPE" "TYRO3 WILD-TYPE" "TYRO3 WILD-TYPE" "TYRO3 WILD-TYPE" 
     TCGA-RQ-A6JB      TCGA-RQ-AAAT      TCGA-VB-A8QN 
"TYRO3 WILD-TYPE" "TYRO3 WILD-TYPE" "TYRO3 WILD-TYPE" 
D31V4, binary
                 cls
clus               0  1
  TYRO3 MUTATED    0  4
  TYRO3 WILD-TYPE 26 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRO3 MUTATED      0    4
  TYRO3 WILD-TYPE   26   18
        clus
vv       TYRO3 MUTATED TYRO3 WILD-TYPE
  FEMALE             0              26
  MALE               4              18
[1] 2 2
[1] FALSE
D31V5, binary
                 cls
clus               0  1
  TYRO3 MUTATED    4  0
  TYRO3 WILD-TYPE 36  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRO3 MUTATED      4    0
  TYRO3 WILD-TYPE   36    7
     clus
vv    TYRO3 MUTATED TYRO3 WILD-TYPE
  NO              4              36
  YES             0               7
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  TYRO3 MUTATED                                                                                   4
  TYRO3 WILD-TYPE                                                                                37
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  TYRO3 MUTATED                          0                                  0
  TYRO3 WILD-TYPE                        3                                  4
D31V6, multiclass
                                                                                   clus
vv                                                                                  TYRO3 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                                                                                  TYRO3 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              37
  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
  TYRO3 MUTATED       1                         0     3
  TYRO3 WILD-TYPE    17                         1    26
D31V7, multiclass
                           clus
vv                          TYRO3 MUTATED TYRO3 WILD-TYPE
  ASIAN                                 1              17
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 3              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, binary
                 cls
clus               0  1
  TYRO3 MUTATED    0  4
  TYRO3 WILD-TYPE 12 32
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TYRO3 MUTATED      0    4
  TYRO3 WILD-TYPE   12   32
                        clus
vv                       TYRO3 MUTATED TYRO3 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             4              32
[1] 2 2
[1] FALSE

Clustering(32) Variable = GSTZ1 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2              0  1
  GSTZ1 MUTATED    2  1
  GSTZ1 WILD-TYPE 36  8
  GSTZ1 MUTATED GSTZ1 WILD-TYPE 
              3              44 
  GSTZ1 MUTATED GSTZ1 WILD-TYPE 
              1               8 
$`GSTZ1 MUTATED`
TCGA-G8-6325 TCGA-G8-6907 TCGA-G8-6914 
       51.98        19.56       196.60 

$`GSTZ1 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-G8-6326 TCGA-G8-6906 
       26.01        12.66        31.96        41.16        70.06       211.23 
TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      116.81       150.51        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-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  GSTZ1 MUTATED GSTZ1 WILD-TYPE 
          19.56            0.03 
  GSTZ1 MUTATED GSTZ1 WILD-TYPE 
         196.60          211.23 
  GSTZ1 MUTATED GSTZ1 WILD-TYPE 
          51.98           26.68 
[1] "19.6 - 196.6 (52.0)" "0.0 - 211.2 (26.7)" 
[1] "hr=" "1.4"
D32V2, continuous
                 vv
clus              ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  GSTZ1 MUTATED         0                  0    0     0      0     0     0
  GSTZ1 WILD-TYPE       2                  2    4     3      1     2     1
                 vv
clus              OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  GSTZ1 MUTATED                       0             0               0
  GSTZ1 WILD-TYPE                     1             1               3
                 vv
clus              SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  GSTZ1 MUTATED                                               0       0       0
  GSTZ1 WILD-TYPE                                             1       2       2
D32V3, multiclass
D32V4, binary
                 cls
clus               0  1
  GSTZ1 MUTATED    1  2
  GSTZ1 WILD-TYPE 25 20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTZ1 MUTATED      1    2
  GSTZ1 WILD-TYPE   25   20
        clus
vv       GSTZ1 MUTATED GSTZ1 WILD-TYPE
  FEMALE             1              25
  MALE               2              20
[1] 2 2
[1] FALSE
D32V5, binary
                 cls
clus               0  1
  GSTZ1 MUTATED    3  0
  GSTZ1 WILD-TYPE 37  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTZ1 MUTATED      3    0
  GSTZ1 WILD-TYPE   37    7
     clus
vv    GSTZ1 MUTATED GSTZ1 WILD-TYPE
  NO              3              37
  YES             0               7
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  GSTZ1 MUTATED                                                                                   3
  GSTZ1 WILD-TYPE                                                                                38
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  GSTZ1 MUTATED                          0                                  0
  GSTZ1 WILD-TYPE                        3                                  4
D32V6, multiclass
                                                                                   clus
vv                                                                                  GSTZ1 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                                                                                  GSTZ1 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              38
  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
  GSTZ1 MUTATED       0                         0     3
  GSTZ1 WILD-TYPE    18                         1    26
D32V7, multiclass
                           clus
vv                          GSTZ1 MUTATED GSTZ1 WILD-TYPE
  ASIAN                                 0              18
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 3              26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, binary
                 cls
clus               0  1
  GSTZ1 MUTATED    0  3
  GSTZ1 WILD-TYPE 12 33
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTZ1 MUTATED      0    3
  GSTZ1 WILD-TYPE   12   33
                        clus
vv                       GSTZ1 MUTATED GSTZ1 WILD-TYPE
  HISPANIC OR LATINO                 0              12
  NOT HISPANIC OR LATINO             3              33
[1] 2 2
[1] FALSE

Clustering(33) Variable = STAT3 MUTATION ANALYSIS
D33V1, survival
                 sevent
clus2              0  1
  STAT3 MUTATED    5  1
  STAT3 WILD-TYPE 33  8
  STAT3 MUTATED STAT3 WILD-TYPE 
              6              41 
  STAT3 MUTATED STAT3 WILD-TYPE 
              1               8 
$`STAT3 MUTATED`
TCGA-FA-A6HN TCGA-FF-8061 TCGA-GR-7351 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
        1.91        27.35       150.51        25.91         0.03         0.56 

$`STAT3 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-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
        4.14        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       31.96        41.16        51.98        70.06       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      116.81       196.60        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 
       45.14       109.58        25.15       111.58        12.85 

  STAT3 MUTATED STAT3 WILD-TYPE 
           0.03            4.14 
  STAT3 MUTATED STAT3 WILD-TYPE 
         150.51          211.23 
  STAT3 MUTATED STAT3 WILD-TYPE 
          13.91           31.73 
[1] "0.0 - 150.5 (13.9)" "4.1 - 211.2 (31.7)"
[1] "hr=" "1.4"
D33V2, continuous
                 vv
clus              ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  STAT3 MUTATED         0                  0    1     2      0     0     0
  STAT3 WILD-TYPE       2                  2    3     1      1     2     1
                 vv
clus              OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  STAT3 MUTATED                       0             0               1
  STAT3 WILD-TYPE                     1             1               2
                 vv
clus              SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  STAT3 MUTATED                                               0       1       1
  STAT3 WILD-TYPE                                             1       1       1
D33V3, multiclass
                                               clus
vv                                              STAT3 MUTATED STAT3 WILD-TYPE
  ADRENAL                                                   0               2
  ASCITES/PERITONEUM                                        0               2
  BONE                                                      1               3
  BRAIN                                                     2               1
  BREAST                                                    0               1
  COLON                                                     0               2
  LIVER                                                     0               1
  OTHER EXTRANODAL SITE                                     0               1
  PAROTID GLAND                                             0               1
  SMALL INTESTINE                                           1               2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)             0               1
  STOMACH                                                   1               1
  THYROID                                                   1               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V4, binary
                 cls
clus               0  1
  STAT3 MUTATED    3  4
  STAT3 WILD-TYPE 23 18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT3 MUTATED      3    4
  STAT3 WILD-TYPE   23   18
        clus
vv       STAT3 MUTATED STAT3 WILD-TYPE
  FEMALE             3              23
  MALE               4              18
[1] 2 2
[1] FALSE
D33V5, binary
                 cls
clus               0  1
  STAT3 MUTATED    5  1
  STAT3 WILD-TYPE 35  6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT3 MUTATED      5    1
  STAT3 WILD-TYPE   35    6
     clus
vv    STAT3 MUTATED STAT3 WILD-TYPE
  NO              5              35
  YES             1               6
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  STAT3 MUTATED                                                                                   4
  STAT3 WILD-TYPE                                                                                37
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  STAT3 MUTATED                          3                                  0
  STAT3 WILD-TYPE                        0                                  4
D33V6, multiclass
                                                                                   clus
vv                                                                                  STAT3 MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             4
  PRIMARY DLBCL OF THE CNS                                                                      3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                            0
                                                                                   clus
vv                                                                                  STAT3 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              37
  PRIMARY DLBCL OF THE CNS                                                                        0
  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
  STAT3 MUTATED       2                         0     5
  STAT3 WILD-TYPE    16                         1    24
D33V7, multiclass
                           clus
vv                          STAT3 MUTATED STAT3 WILD-TYPE
  ASIAN                                 2              16
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 5              24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, binary
                 cls
clus               0  1
  STAT3 MUTATED    2  5
  STAT3 WILD-TYPE 10 31
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT3 MUTATED      2    5
  STAT3 WILD-TYPE   10   31
                        clus
vv                       STAT3 MUTATED STAT3 WILD-TYPE
  HISPANIC OR LATINO                 2              10
  NOT HISPANIC OR LATINO             5              31
[1] 2 2
[1] FALSE

Clustering(34) Variable = IRF8 MUTATION ANALYSIS
D34V1, survival
                sevent
clus2             0  1
  IRF8 MUTATED    3  2
  IRF8 WILD-TYPE 35  7
  IRF8 MUTATED IRF8 WILD-TYPE 
             5             42 
  IRF8 MUTATED IRF8 WILD-TYPE 
             2              7 
$`IRF8 MUTATED`
TCGA-G8-6906 TCGA-G8-6909 TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-RQ-A6JB 
      211.23       116.81       109.58        25.15         0.03 

$`IRF8 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-G8-6325 TCGA-G8-6326 
       26.01        12.66        31.96        41.16        51.98        70.06 
TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
       19.56       196.60       150.51        98.07        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-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-AAAT 
       53.16        45.14       111.58        12.85        25.91         0.56 

  IRF8 MUTATED IRF8 WILD-TYPE 
          0.03           0.56 
  IRF8 MUTATED IRF8 WILD-TYPE 
        211.23         196.60 
  IRF8 MUTATED IRF8 WILD-TYPE 
        109.58          26.68 
[1] "0.0 - 211.2 (109.6)" "0.6 - 196.6 (26.7)" 
[1] "hr=" "1.3"
D34V2, continuous
                vv
clus             ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  IRF8 MUTATED         0                  0    1     0      0     0     0
  IRF8 WILD-TYPE       2                  2    3     3      1     2     1
                vv
clus             OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  IRF8 MUTATED                       1             0               0
  IRF8 WILD-TYPE                     0             1               3
                vv
clus             SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  IRF8 MUTATED                                               0       0       0
  IRF8 WILD-TYPE                                             1       2       2
D34V3, multiclass
[1] "Remove cluster labels:" "IRF8 MUTATED"          
clus
  IRF8 MUTATED IRF8 WILD-TYPE 
             2             23 
    TCGA-FA-8693     TCGA-FA-A4BB     TCGA-FA-A4XK     TCGA-FA-A7DS 
"IRF8 WILD-TYPE" "IRF8 WILD-TYPE" "IRF8 WILD-TYPE" "IRF8 WILD-TYPE" 
    TCGA-FA-A82F     TCGA-FF-8043     TCGA-FF-8061     TCGA-FF-8062 
"IRF8 WILD-TYPE" "IRF8 WILD-TYPE" "IRF8 WILD-TYPE" "IRF8 WILD-TYPE" 
    TCGA-FF-A7CQ     TCGA-FF-A7CR     TCGA-FF-A7CW     TCGA-FF-A7CX 
"IRF8 WILD-TYPE" "IRF8 WILD-TYPE" "IRF8 WILD-TYPE" "IRF8 WILD-TYPE" 
    TCGA-FM-8000     TCGA-G8-6324     TCGA-G8-6326     TCGA-GR-7351 
"IRF8 WILD-TYPE" "IRF8 WILD-TYPE" "IRF8 WILD-TYPE" "IRF8 WILD-TYPE" 
    TCGA-GR-A4D4     TCGA-GR-A4D5     TCGA-GR-A4D9     TCGA-GS-A9TT 
"IRF8 WILD-TYPE" "IRF8 WILD-TYPE" "IRF8 WILD-TYPE" "IRF8 WILD-TYPE" 
    TCGA-RQ-A68N     TCGA-RQ-AAAT     TCGA-VB-A8QN 
"IRF8 WILD-TYPE" "IRF8 WILD-TYPE" "IRF8 WILD-TYPE" 
D34V4, binary
                cls
clus              0  1
  IRF8 MUTATED    2  3
  IRF8 WILD-TYPE 24 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF8 MUTATED      2    3
  IRF8 WILD-TYPE   24   19
        clus
vv       IRF8 MUTATED IRF8 WILD-TYPE
  FEMALE            2             24
  MALE              3             19
[1] 2 2
[1] FALSE
D34V5, binary
                cls
clus              0  1
  IRF8 MUTATED    3  1
  IRF8 WILD-TYPE 37  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF8 MUTATED      3    1
  IRF8 WILD-TYPE   37    6
     clus
vv    IRF8 MUTATED IRF8 WILD-TYPE
  NO             3             37
  YES            1              6
[1] 2 2
[1] FALSE
                vv
clus             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  IRF8 MUTATED                                                                                   3
  IRF8 WILD-TYPE                                                                                38
                vv
clus             PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  IRF8 MUTATED                          1                                  1
  IRF8 WILD-TYPE                        2                                  3
D34V6, multiclass
                                                                                   clus
vv                                                                                  IRF8 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                                                                                  IRF8 WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)             38
  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
  IRF8 MUTATED       0                         0     5
  IRF8 WILD-TYPE    18                         1    24
D34V7, multiclass
                           clus
vv                          IRF8 MUTATED IRF8 WILD-TYPE
  ASIAN                                0             18
  BLACK OR AFRICAN AMERICAN            0              1
  WHITE                                5             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, binary
                cls
clus              0  1
  IRF8 MUTATED    2  3
  IRF8 WILD-TYPE 10 33
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF8 MUTATED      2    3
  IRF8 WILD-TYPE   10   33
                        clus
vv                       IRF8 MUTATED IRF8 WILD-TYPE
  HISPANIC OR LATINO                2             10
  NOT HISPANIC OR LATINO            3             33
[1] 2 2
[1] FALSE

Clustering(35) Variable = TMEM30A MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                0  1
  TMEM30A MUTATED    3  1
  TMEM30A WILD-TYPE 35  8
  TMEM30A MUTATED TMEM30A WILD-TYPE 
                4                43 
  TMEM30A MUTATED TMEM30A WILD-TYPE 
                1                 8 
$`TMEM30A MUTATED`
TCGA-FF-8046 TCGA-G8-6906 TCGA-GR-A4D5 TCGA-GS-A9TZ 
       24.69       211.23        42.71        25.15 

$`TMEM30A 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-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-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6907 
       12.66        31.96        41.16        51.98        70.06        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
      116.81       196.60       150.51        98.07        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-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
       45.14       109.58       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  TMEM30A MUTATED TMEM30A WILD-TYPE 
            24.69              0.03 
  TMEM30A MUTATED TMEM30A WILD-TYPE 
           211.23            196.60 
  TMEM30A MUTATED TMEM30A WILD-TYPE 
            33.93             27.35 
[1] "24.7 - 211.2 (33.9)" "0.0 - 196.6 (27.4)" 
[1] "hr="     "8.2e+07"
D35V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  TMEM30A MUTATED         0                  0    1     0      0     0     0
  TMEM30A WILD-TYPE       2                  2    3     3      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  TMEM30A MUTATED                       1             0               0
  TMEM30A WILD-TYPE                     0             1               3
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  TMEM30A MUTATED                                               0       0
  TMEM30A WILD-TYPE                                             1       2
                   vv
clus                THYROID
  TMEM30A MUTATED         0
  TMEM30A WILD-TYPE       2
D35V3, multiclass
[1] "Remove cluster labels:" "TMEM30A MUTATED"       
clus
  TMEM30A MUTATED TMEM30A WILD-TYPE 
                2                23 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A7DS 
"TMEM30A WILD-TYPE" "TMEM30A WILD-TYPE" "TMEM30A WILD-TYPE" "TMEM30A WILD-TYPE" 
       TCGA-FA-A82F        TCGA-FF-8043        TCGA-FF-8061        TCGA-FF-8062 
"TMEM30A WILD-TYPE" "TMEM30A WILD-TYPE" "TMEM30A WILD-TYPE" "TMEM30A WILD-TYPE" 
       TCGA-FF-A7CQ        TCGA-FF-A7CR        TCGA-FF-A7CW        TCGA-FF-A7CX 
"TMEM30A WILD-TYPE" "TMEM30A WILD-TYPE" "TMEM30A WILD-TYPE" "TMEM30A WILD-TYPE" 
       TCGA-FM-8000        TCGA-G8-6324        TCGA-G8-6326        TCGA-GR-7351 
"TMEM30A WILD-TYPE" "TMEM30A WILD-TYPE" "TMEM30A WILD-TYPE" "TMEM30A WILD-TYPE" 
       TCGA-GR-A4D4        TCGA-GR-A4D9        TCGA-GS-A9TT        TCGA-RQ-A68N 
"TMEM30A WILD-TYPE" "TMEM30A WILD-TYPE" "TMEM30A WILD-TYPE" "TMEM30A WILD-TYPE" 
       TCGA-RQ-A6JB        TCGA-RQ-AAAT        TCGA-VB-A8QN 
"TMEM30A WILD-TYPE" "TMEM30A WILD-TYPE" "TMEM30A WILD-TYPE" 
D35V4, binary
                   cls
clus                 0  1
  TMEM30A MUTATED    1  3
  TMEM30A WILD-TYPE 25 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM30A MUTATED      1    3
  TMEM30A WILD-TYPE   25   19
        clus
vv       TMEM30A MUTATED TMEM30A WILD-TYPE
  FEMALE               1                25
  MALE                 3                19
[1] 2 2
[1] FALSE
D35V5, binary
                   cls
clus                 0  1
  TMEM30A MUTATED    3  1
  TMEM30A WILD-TYPE 37  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM30A MUTATED      3    1
  TMEM30A WILD-TYPE   37    6
     clus
vv    TMEM30A MUTATED TMEM30A WILD-TYPE
  NO                3                37
  YES               1                 6
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  TMEM30A MUTATED                                                                                   3
  TMEM30A WILD-TYPE                                                                                38
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  TMEM30A MUTATED                          0                                  1
  TMEM30A WILD-TYPE                        3                                  3
D35V6, multiclass
                                                                                   clus
vv                                                                                  TMEM30A 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                                                                                  TMEM30A WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                38
  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
  TMEM30A MUTATED       1                         0     3
  TMEM30A WILD-TYPE    17                         1    26
D35V7, multiclass
                           clus
vv                          TMEM30A MUTATED TMEM30A WILD-TYPE
  ASIAN                                   1                17
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, binary
                   cls
clus                 0  1
  TMEM30A MUTATED    1  3
  TMEM30A WILD-TYPE 11 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM30A MUTATED      1    3
  TMEM30A WILD-TYPE   11   33
                        clus
vv                       TMEM30A MUTATED TMEM30A WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               3                33
[1] 2 2
[1] FALSE

Clustering(36) Variable = UBE2A MUTATION ANALYSIS
D36V1, survival
                 sevent
clus2              0  1
  UBE2A MUTATED    3  0
  UBE2A WILD-TYPE 35  9
  UBE2A MUTATED UBE2A WILD-TYPE 
              3              44 
  UBE2A MUTATED UBE2A WILD-TYPE 
              0               9 
$`UBE2A MUTATED`
TCGA-FF-8041 TCGA-FF-8047 TCGA-RQ-AAAT 
       35.54         4.14         0.56 

$`UBE2A 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-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       31.96        41.16        51.98        70.06       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
      116.81       196.60       150.51        98.07        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 
       25.91         0.03 

  UBE2A MUTATED UBE2A WILD-TYPE 
           0.56            0.03 
  UBE2A MUTATED UBE2A WILD-TYPE 
          35.54          211.23 
  UBE2A MUTATED UBE2A WILD-TYPE 
          4.140          29.225 
[1] "0.6 - 35.5 (4.1)"   "0.0 - 211.2 (29.2)"
[1] "hr="     "2.5e+07"
D36V2, continuous
                 vv
clus              ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  UBE2A MUTATED         0                  0    0     1      0     0     0
  UBE2A WILD-TYPE       2                  2    4     2      1     2     1
                 vv
clus              OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  UBE2A MUTATED                       0             0               0
  UBE2A WILD-TYPE                     1             1               3
                 vv
clus              SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  UBE2A MUTATED                                               0       1       0
  UBE2A WILD-TYPE                                             1       1       2
D36V3, multiclass
[1] "Remove cluster labels:" "UBE2A MUTATED"         
clus
  UBE2A MUTATED UBE2A WILD-TYPE 
              2              23 
     TCGA-FA-8693      TCGA-FA-A4BB      TCGA-FA-A4XK      TCGA-FA-A7DS 
"UBE2A WILD-TYPE" "UBE2A WILD-TYPE" "UBE2A WILD-TYPE" "UBE2A WILD-TYPE" 
     TCGA-FA-A82F      TCGA-FF-8043      TCGA-FF-8061      TCGA-FF-8062 
"UBE2A WILD-TYPE" "UBE2A WILD-TYPE" "UBE2A WILD-TYPE" "UBE2A WILD-TYPE" 
     TCGA-FF-A7CQ      TCGA-FF-A7CR      TCGA-FF-A7CW      TCGA-FF-A7CX 
"UBE2A WILD-TYPE" "UBE2A WILD-TYPE" "UBE2A WILD-TYPE" "UBE2A WILD-TYPE" 
     TCGA-FM-8000      TCGA-G8-6324      TCGA-G8-6326      TCGA-G8-6906 
"UBE2A WILD-TYPE" "UBE2A WILD-TYPE" "UBE2A WILD-TYPE" "UBE2A WILD-TYPE" 
     TCGA-GR-7351      TCGA-GR-A4D4      TCGA-GR-A4D5      TCGA-GR-A4D9 
"UBE2A WILD-TYPE" "UBE2A WILD-TYPE" "UBE2A WILD-TYPE" "UBE2A WILD-TYPE" 
     TCGA-GS-A9TT      TCGA-RQ-A68N      TCGA-RQ-A6JB 
"UBE2A WILD-TYPE" "UBE2A WILD-TYPE" "UBE2A WILD-TYPE" 
D36V4, binary
                 cls
clus               0  1
  UBE2A MUTATED    3  1
  UBE2A WILD-TYPE 23 21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBE2A MUTATED      3    1
  UBE2A WILD-TYPE   23   21
        clus
vv       UBE2A MUTATED UBE2A WILD-TYPE
  FEMALE             3              23
  MALE               1              21
[1] 2 2
[1] FALSE
D36V5, binary
                 cls
clus               0  1
  UBE2A MUTATED    4  0
  UBE2A WILD-TYPE 36  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBE2A MUTATED      4    0
  UBE2A WILD-TYPE   36    7
     clus
vv    UBE2A MUTATED UBE2A WILD-TYPE
  NO              4              36
  YES             0               7
[1] 2 2
[1] FALSE
                 vv
clus              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  UBE2A MUTATED                                                                                   2
  UBE2A WILD-TYPE                                                                                39
                 vv
clus              PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  UBE2A MUTATED                          1                                  1
  UBE2A WILD-TYPE                        2                                  3
D36V6, multiclass
                                                                                   clus
vv                                                                                  UBE2A 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                                                            1
                                                                                   clus
vv                                                                                  UBE2A WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              39
  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
  UBE2A MUTATED       2                         0     2
  UBE2A WILD-TYPE    16                         1    27
D36V7, multiclass
                           clus
vv                          UBE2A MUTATED UBE2A WILD-TYPE
  ASIAN                                 2              16
  BLACK OR AFRICAN AMERICAN             0               1
  WHITE                                 2              27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, binary
                 cls
clus               0  1
  UBE2A MUTATED    1  3
  UBE2A WILD-TYPE 11 33
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBE2A MUTATED      1    3
  UBE2A WILD-TYPE   11   33
                        clus
vv                       UBE2A MUTATED UBE2A WILD-TYPE
  HISPANIC OR LATINO                 1              11
  NOT HISPANIC OR LATINO             3              33
[1] 2 2
[1] FALSE
