[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/15078461/DLBC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/15082594/transformed.cor.cli.txt"

nPatients in clinical file=47, in cluster file=48, common to both=47
[1] "Reduce the number of clustering variables from 82 to 52."
[1] 52 47
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                5                42 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                5                42 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                41 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                41 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                41 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                41 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10                37 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10                37 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               13                34 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               13                34 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                40 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                40 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6                41 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6                41 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6                41 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6                41 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4                43 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4                43 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               15                32 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               15                32 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               13                34 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               13                34 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7                40 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7                40 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                8                39 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                8                39 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                7                40 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                7                40 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7                40 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7                40 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 43 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 43 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                 43 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                 43 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                 38 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                 38 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                13                 34 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                13                 34 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 7                 40 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 7                 40 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 9                 38 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 9                 38 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                 42 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                 42 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                 40 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                 40 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                 40 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                 40 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                 44 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                 44 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                13                 34 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                13                 34 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                14                 33 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                14                 33 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                 44 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                 44 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                 44 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                 44 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 5                 42 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 5                 42 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 4                 43 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 4                 43 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                 37 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                 37 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                6                41 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                6                41 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                41 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                41 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                44 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                44 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                42 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                42 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4                43 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4                43 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                3                44 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                3                44 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4                43 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4                43 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7                40 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7                40 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                8                39 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                8                39 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                43 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                43 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 3                 44 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 3                 44 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                 40 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                 40 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 43 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 43 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 9                 38 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 9                 38 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                 43 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                 43 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                 42 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                 42 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 43 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 43 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                 44 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                 44 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                5                42 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                5                42 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                43 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                43 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "NEOPLASM_DISEASESTAGE"                 
 [6] "PATHOLOGY_T_STAGE"                     
 [7] "PATHOLOGY_N_STAGE"                     
 [8] "PATHOLOGY_M_STAGE"                     
 [9] "DCC_UPLOAD_DATE"                       
[10] "GENDER"                                
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[12] "RADIATION_THERAPY"                     
[13] "HISTOLOGICAL_TYPE"                     
[14] "RADIATIONS_RADIATION_REGIMENINDICATION"
[15] "RACE"                                  
[16] "ETHNICITY"                             
[17] "BATCH_NUMBER"                          

Input Data has 17 rows and 47 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=33,	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=41,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'NEOPLASM_DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NEOPLASM_DISEASESTAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE 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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "1"     "46"   
freq.contrast "46"    "1"    
both >= 3     "FALSE" "FALSE"
Variable 15:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'BATCH_NUMBER':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 47 columns, 1 survival variables, and 5 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"    "GENDER"            "HISTOLOGICAL_TYPE"
[4] "RACE"              "ETHNICITY"        
YEARS_TO_BIRTH, nv=33, binary=FALSE, numeric=TRUE
GENDER, 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 = 1Q GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED    5  0
  1Q GAIN WILD-TYPE 32  9
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                5                41 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                0                 9 
$`1Q GAIN MUTATED`
TCGA-FM-8000 TCGA-G8-6325 TCGA-GR-7353 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       31.96        51.98        98.07        57.17        27.32 

$`1Q GAIN 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        13.15        13.48 
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-G8-6324 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       12.66        41.16        47.38       211.23        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GS-A9TT 
      196.60       150.51        36.13        42.71        43.86        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
      112.24        18.25        47.84        37.22       109.58        21.70 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       89.33        12.85        25.91         0.03         0.56 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            27.32              0.03 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            98.07            211.23 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            51.98             25.91 
[1] "27.3 - 98.1 (52.0)" "0.0 - 211.2 (25.9)"
[1] "hr="     "2.3e+08"
D1V2, continuous
D1V3, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    3  2
  1Q GAIN WILD-TYPE 23 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3    2
  1Q GAIN WILD-TYPE   23   19
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               3                23
  MALE                 2                19
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  1Q GAIN MUTATED                                                                                   5
  1Q GAIN WILD-TYPE                                                                                35
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  1Q GAIN MUTATED                          0                                  0
  1Q GAIN WILD-TYPE                        3                                  4
D1V4, multiclass
                                                                                   clus
vv                                                                                  1Q GAIN 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                                                                                  1Q GAIN 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
  1Q GAIN MUTATED       0                         0     5
  1Q GAIN WILD-TYPE    18                         1    23
D1V5, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   0                18
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   5                23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    1  4
  1Q GAIN WILD-TYPE 11 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1    4
  1Q GAIN WILD-TYPE   11   31
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               4                31
[1] 2 2
[1] FALSE

Clustering(2) Variable = 2P GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    5  1
  2P GAIN WILD-TYPE 32  8
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                40 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                1                 8 
$`2P GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A82F TCGA-FF-8041 TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
       23.28        14.04        35.54        37.22       109.58        21.70 

$`2P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         1.91        13.15        13.48         8.15 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       31.10        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66        31.96        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        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        36.13        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9U3 
       27.32        38.24       112.24        18.25        47.84        89.33 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85        25.91         0.03         0.56 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            14.04              0.03 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           109.58            211.23 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           29.410            27.335 
[1] "14.0 - 109.6 (29.4)" "0.0 - 211.2 (27.3)" 
[1] "hr=" "1"  
D2V2, continuous
D2V3, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    3  3
  2P GAIN WILD-TYPE 23 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3    3
  2P GAIN WILD-TYPE   23   18
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               3                23
  MALE                 3                18
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  2P GAIN MUTATED                                                                                   4
  2P GAIN WILD-TYPE                                                                                36
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  2P GAIN MUTATED                          0                                  2
  2P GAIN WILD-TYPE                        3                                  2
D2V4, multiclass
                                                                                   clus
vv                                                                                  2P GAIN 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                                                                                  2P GAIN 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
  2P GAIN MUTATED       3                         0     3
  2P GAIN WILD-TYPE    15                         1    25
D2V5, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                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"
D2V6, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    3  3
  2P GAIN WILD-TYPE  9 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3    3
  2P GAIN WILD-TYPE    9   32
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO               3                32
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2Q GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    5  1
  2Q GAIN WILD-TYPE 32  8
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                40 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                1                 8 
$`2Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A82F TCGA-FF-8041 TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
       23.28        14.04        35.54        37.22       109.58        21.70 

$`2Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         1.91        13.15        13.48         8.15 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       31.10        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66        31.96        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        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        36.13        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9U3 
       27.32        38.24       112.24        18.25        47.84        89.33 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85        25.91         0.03         0.56 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            14.04              0.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           109.58            211.23 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           29.410            27.335 
[1] "14.0 - 109.6 (29.4)" "0.0 - 211.2 (27.3)" 
[1] "hr=" "1"  
D3V2, continuous
D3V3, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    3  3
  2Q GAIN WILD-TYPE 23 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3    3
  2Q GAIN WILD-TYPE   23   18
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               3                23
  MALE                 3                18
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  2Q GAIN MUTATED                                                                                   4
  2Q GAIN WILD-TYPE                                                                                36
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  2Q GAIN MUTATED                          0                                  2
  2Q GAIN WILD-TYPE                        3                                  2
D3V4, multiclass
                                                                                   clus
vv                                                                                  2Q GAIN 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                                                                                  2Q GAIN 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
  2Q GAIN MUTATED       3                         0     3
  2Q GAIN WILD-TYPE    15                         1    25
D3V5, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                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"
D3V6, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    3  3
  2Q GAIN WILD-TYPE  9 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3    3
  2Q GAIN WILD-TYPE    9   32
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO               3                32
[1] 2 2
[1] FALSE

Clustering(4) Variable = 3P GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED   10  0
  3P GAIN WILD-TYPE 27  9
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10                36 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                0                 9 
$`3P GAIN MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-A7CW TCGA-G8-6914 TCGA-GR-A4D6 
       13.15        14.04        31.10        26.01       196.60        43.86 
TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9U3 TCGA-RQ-A68N 
       47.84        37.22        89.33        25.91 

$`3P GAIN 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        13.48         8.15 
TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
        9.80        10.29        12.66        31.96        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-7353 
       47.38       211.23        19.56       116.81       150.51        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU 
       36.13        42.71        57.17        27.32        38.24       112.24 
TCGA-GS-A9TV TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U4 TCGA-RQ-A6JB TCGA-RQ-AAAT 
       18.25       109.58        21.70        12.85         0.03         0.56 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            13.15              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           196.60            211.23 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           34.160            26.005 
[1] "13.2 - 196.6 (34.2)" "0.0 - 211.2 (26.0)" 
[1] "hr="     "2.9e+08"
D4V2, continuous
D4V3, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    6  4
  3P GAIN WILD-TYPE 20 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      6    4
  3P GAIN WILD-TYPE   20   17
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               6                20
  MALE                 4                17
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  3P GAIN MUTATED                                                                                   8
  3P GAIN WILD-TYPE                                                                                32
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  3P GAIN MUTATED                          1                                  1
  3P GAIN WILD-TYPE                        2                                  3
D4V4, multiclass
                                                                                   clus
vv                                                                                  3P GAIN MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               8
  PRIMARY DLBCL OF THE CNS                                                                        1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              1
                                                                                   clus
vv                                                                                  3P GAIN WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                32
  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
  3P GAIN MUTATED       5                         0     5
  3P GAIN WILD-TYPE    13                         1    23
D4V5, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   5                13
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   5                23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    4  6
  3P GAIN WILD-TYPE  8 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4    6
  3P GAIN WILD-TYPE    8   29
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 8
  NOT HISPANIC OR LATINO               6                29
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3Q GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED   12  0
  3Q GAIN WILD-TYPE 25  9
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               12                34 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                0                 9 
$`3Q GAIN MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8047 TCGA-FF-A7CW TCGA-G8-6914 
       13.15        14.04        31.10         4.14        26.01       196.60 
TCGA-GR-A4D6 TCGA-GS-A9TU TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9U3 TCGA-RQ-A68N 
       43.86       112.24        47.84        37.22        89.33        25.91 

$`3Q GAIN 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        13.48         8.15 
TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       35.54        31.73        24.69        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       10.29        12.66        31.96        41.16        51.98        47.38 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 
      211.23        19.56       116.81       150.51        98.07        36.13 
TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TV TCGA-GS-A9TY 
       42.71        57.17        27.32        38.24        18.25       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U4 TCGA-RQ-A6JB TCGA-RQ-AAAT 
       21.70        12.85         0.03         0.56 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             4.14              0.03 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           196.60            211.23 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           34.160            26.005 
[1] "4.1 - 196.6 (34.2)" "0.0 - 211.2 (26.0)"
[1] "hr="     "3.2e+08"
D5V2, continuous
D5V3, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    8  5
  3Q GAIN WILD-TYPE 18 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      8    5
  3Q GAIN WILD-TYPE   18   16
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               8                18
  MALE                 5                16
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  3Q GAIN MUTATED                                                                                  11
  3Q GAIN WILD-TYPE                                                                                29
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  3Q GAIN MUTATED                          1                                  1
  3Q GAIN WILD-TYPE                        2                                  3
D5V4, multiclass
                                                                                   clus
vv                                                                                  3Q GAIN MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              11
  PRIMARY DLBCL OF THE CNS                                                                        1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              1
                                                                                   clus
vv                                                                                  3Q GAIN WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                29
  PRIMARY DLBCL OF THE CNS                                                                          2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       6                         0     7
  3Q GAIN WILD-TYPE    12                         1    21
D5V5, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   6                12
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   7                21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    5  8
  3Q GAIN WILD-TYPE  7 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5    8
  3Q GAIN WILD-TYPE    7   27
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 7
  NOT HISPANIC OR LATINO               8                27
[1] 2 2
[1] FALSE

Clustering(6) Variable = 5P GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    5  2
  5P GAIN WILD-TYPE 32  7
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                39 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                 7 
$`5P GAIN MUTATED`
TCGA-FA-A7Q1 TCGA-FF-8041 TCGA-G8-6909 TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
        8.15        35.54       116.81        47.84        37.22       109.58 
TCGA-GS-A9TZ 
       21.70 

$`5P GAIN 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        13.15        13.48 
TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       14.04        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-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6914 
       41.16        51.98        47.38       211.23        19.56       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      150.51        98.07        36.13        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9U3 TCGA-GS-A9U4 
       27.32        38.24       112.24        18.25        89.33        12.85 
TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.91         0.03         0.56 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             8.15              0.03 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           116.81            211.23 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            37.22             26.01 
[1] "8.2 - 116.8 (37.2)" "0.0 - 211.2 (26.0)"
[1] "hr=" "1.5"
D6V2, continuous
D6V3, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    4  3
  5P GAIN WILD-TYPE 22 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      4    3
  5P GAIN WILD-TYPE   22   18
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               4                22
  MALE                 3                18
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  5P GAIN MUTATED                                                                                   4
  5P GAIN WILD-TYPE                                                                                36
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  5P GAIN MUTATED                          0                                  3
  5P GAIN WILD-TYPE                        3                                  1
D6V4, multiclass
                                                                                   clus
vv                                                                                  5P GAIN 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                                                              3
                                                                                   clus
vv                                                                                  5P GAIN 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                                                                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
  5P GAIN MUTATED       2                         0     5
  5P GAIN WILD-TYPE    16                         1    23
D6V5, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   2                16
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   5                23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    4  3
  5P GAIN WILD-TYPE  8 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      4    3
  5P GAIN WILD-TYPE    8   32
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 8
  NOT HISPANIC OR LATINO               3                32
[1] 2 2
[1] FALSE

Clustering(7) Variable = 5Q GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED    5  1
  5Q GAIN WILD-TYPE 32  8
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6                40 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                1                 8 
$`5Q GAIN MUTATED`
TCGA-FA-A7Q1 TCGA-FF-8041 TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
        8.15        35.54        47.84        37.22       109.58        21.70 

$`5Q GAIN 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        13.15        13.48 
TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       14.04        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-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        47.38       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        36.13        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9U3 
       57.17        27.32        38.24       112.24        18.25        89.33 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85        25.91         0.03         0.56 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             8.15              0.03 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           109.58            211.23 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           36.380            26.665 
[1] "8.2 - 109.6 (36.4)" "0.0 - 211.2 (26.7)"
[1] "hr=" "1"  
D7V2, continuous
D7V3, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    4  2
  5Q GAIN WILD-TYPE 22 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      4    2
  5Q GAIN WILD-TYPE   22   19
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               4                22
  MALE                 2                19
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  5Q GAIN MUTATED                                                                                   3
  5Q GAIN WILD-TYPE                                                                                37
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  5Q GAIN MUTATED                          0                                  3
  5Q GAIN WILD-TYPE                        3                                  1
D7V4, multiclass
                                                                                   clus
vv                                                                                  5Q GAIN 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                                                              3
                                                                                   clus
vv                                                                                  5Q GAIN 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                                                                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
  5Q GAIN MUTATED       2                         0     4
  5Q GAIN WILD-TYPE    16                         1    24
D7V5, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   2                16
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   4                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"
D7V6, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    4  2
  5Q GAIN WILD-TYPE  8 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      4    2
  5Q GAIN WILD-TYPE    8   33
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 8
  NOT HISPANIC OR LATINO               2                33
[1] 2 2
[1] FALSE

Clustering(8) Variable = 6P GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED    6  0
  6P GAIN WILD-TYPE 31  9
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6                40 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                0                 9 
$`6P GAIN MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8042 TCGA-G8-6325 TCGA-GS-A9TQ TCGA-GS-A9TW 
       13.15        14.04        31.10        51.98        27.32        47.84 

$`6P GAIN 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        13.48         8.15 
TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66        31.96        41.16 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       47.38       211.23        19.56       116.81       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT 
       98.07        36.13        42.71        43.86        57.17        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 
      112.24        18.25        37.22       109.58        21.70        89.33 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85        25.91         0.03         0.56 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            13.15              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            51.98            211.23 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            29.21             26.68 
[1] "13.2 - 52.0 (29.2)" "0.0 - 211.2 (26.7)"
[1] "hr="     "8.5e+07"
D8V2, continuous
D8V3, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    5  1
  6P GAIN WILD-TYPE 21 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5    1
  6P GAIN WILD-TYPE   21   20
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               5                21
  MALE                 1                20
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  6P GAIN MUTATED                                                                                   5
  6P GAIN WILD-TYPE                                                                                35
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  6P GAIN MUTATED                          0                                  1
  6P GAIN WILD-TYPE                        3                                  3
D8V4, multiclass
                                                                                   clus
vv                                                                                  6P GAIN MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               5
  PRIMARY DLBCL OF THE CNS                                                                        0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              1
                                                                                   clus
vv                                                                                  6P GAIN 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
  6P GAIN MUTATED       3                         0     3
  6P GAIN WILD-TYPE    15                         1    25
D8V5, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                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"
D8V6, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    2  4
  6P GAIN WILD-TYPE 10 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2    4
  6P GAIN WILD-TYPE   10   31
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO               4                31
[1] 2 2
[1] FALSE

Clustering(9) Variable = 6Q GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED    4  0
  6Q GAIN WILD-TYPE 33  9
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4                42 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                0                 9 
$`6Q GAIN MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8042 TCGA-GS-A9TQ 
       13.15        14.04        31.10        27.32 

$`6Q GAIN 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        13.48         8.15 
TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66        31.96        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        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        36.13        42.71        43.86        57.17 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       112.24        18.25        47.84        37.22       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       21.70        89.33        12.85        25.91         0.03         0.56 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            13.15              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            31.10            211.23 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            20.68             29.54 
[1] "13.2 - 31.1 (20.7)" "0.0 - 211.2 (29.5)"
[1] "hr="     "7.7e+07"
D9V2, continuous
D9V3, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    4  0
  6Q GAIN WILD-TYPE 22 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      4    0
  6Q GAIN WILD-TYPE   22   21
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               4                22
  MALE                 0                21
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  6Q GAIN MUTATED                                                                                   4
  6Q GAIN WILD-TYPE                                                                                36
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  6Q GAIN MUTATED                          0                                  0
  6Q GAIN WILD-TYPE                        3                                  4
D9V4, multiclass
                                                                                   clus
vv                                                                                  6Q GAIN 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                                                                                  6Q GAIN 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
  6Q GAIN MUTATED       3                         0     1
  6Q GAIN WILD-TYPE    15                         1    27
D9V5, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   1                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"
D9V6, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    1  3
  6Q GAIN WILD-TYPE 11 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    3
  6Q GAIN WILD-TYPE   11   32
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               3                32
[1] 2 2
[1] FALSE

Clustering(10) Variable = 7P GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   14  1
  7P GAIN WILD-TYPE 23  8
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               15                31 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                1                 8 
$`7P GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-A7CW TCGA-FM-8000 
       23.28        13.15        14.04        31.10        26.01        31.96 
TCGA-G8-6914 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GS-A9TQ TCGA-GS-A9TU 
      196.60        98.07        36.13        43.86        27.32       112.24 
TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9U3 
       37.22       109.58        89.33 

$`7P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FF-8041 
        4.34         4.34         1.91        13.48         8.15        35.54 
TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       31.73        24.69         4.14        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       10.29        12.66        41.16        51.98        47.38       211.23 
TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TT 
       19.56       116.81       150.51        42.71        57.17        38.24 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TZ TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
       18.25        47.84        21.70        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            13.15              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           196.60            211.23 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            36.13             22.32 
[1] "13.2 - 196.6 (36.1)" "0.0 - 211.2 (22.3)" 
[1] "hr=" "4.4"
D10V2, continuous
D10V3, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    9  6
  7P GAIN WILD-TYPE 17 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      9    6
  7P GAIN WILD-TYPE   17   15
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               9                17
  MALE                 6                15
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  7P GAIN MUTATED                                                                                  15
  7P GAIN WILD-TYPE                                                                                25
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  7P GAIN MUTATED                          0                                  0
  7P GAIN WILD-TYPE                        3                                  4
D10V4, multiclass
                                                                                   clus
vv                                                                                  7P GAIN MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              15
  PRIMARY DLBCL OF THE CNS                                                                        0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              0
                                                                                   clus
vv                                                                                  7P GAIN WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                25
  PRIMARY DLBCL OF THE CNS                                                                          3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                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
  7P GAIN MUTATED       6                         0     9
  7P GAIN WILD-TYPE    12                         1    19
D10V5, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   6                12
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   9                19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    5 10
  7P GAIN WILD-TYPE  7 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5   10
  7P GAIN WILD-TYPE    7   25
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 7
  NOT HISPANIC OR LATINO              10                25
[1] 2 2
[1] FALSE

Clustering(11) Variable = 7Q GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   12  1
  7Q GAIN WILD-TYPE 25  8
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               13                33 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                1                 8 
$`7Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-A7CW TCGA-FM-8000 
       23.28        13.15        14.04        31.10        26.01        31.96 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GS-A9TQ TCGA-GS-A9TU TCGA-GS-A9TX 
       98.07        36.13        43.86        27.32       112.24        37.22 
TCGA-GS-A9TY 
      109.58 

$`7Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FF-8041 
        4.34         4.34         1.91        13.48         8.15        35.54 
TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       31.73        24.69         4.14        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       10.29        12.66        41.16        51.98        47.38       211.23 
TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D5 TCGA-GR-A4D9 
       19.56       116.81       196.60       150.51        42.71        57.17 
TCGA-GS-A9TT TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 
       38.24        18.25        47.84        21.70        89.33        12.85 
TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.91         0.03         0.56 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            13.15              0.03 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           112.24            211.23 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            31.96             24.69 
[1] "13.2 - 112.2 (32.0)" "0.0 - 211.2 (24.7)" 
[1] "hr=" "3"  
D11V2, continuous
D11V3, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    8  5
  7Q GAIN WILD-TYPE 18 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      8    5
  7Q GAIN WILD-TYPE   18   16
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               8                18
  MALE                 5                16
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  7Q GAIN MUTATED                                                                                  13
  7Q GAIN WILD-TYPE                                                                                27
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  7Q GAIN MUTATED                          0                                  0
  7Q GAIN WILD-TYPE                        3                                  4
D11V4, multiclass
                                                                                   clus
vv                                                                                  7Q GAIN MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              13
  PRIMARY DLBCL OF THE CNS                                                                        0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              0
                                                                                   clus
vv                                                                                  7Q GAIN 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
  7Q GAIN MUTATED       6                         0     7
  7Q GAIN WILD-TYPE    12                         1    21
D11V5, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   6                12
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   7                21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    4  9
  7Q GAIN WILD-TYPE  8 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4    9
  7Q GAIN WILD-TYPE    8   26
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 8
  NOT HISPANIC OR LATINO               9                26
[1] 2 2
[1] FALSE

Clustering(12) Variable = 8P GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED    6  1
  8P GAIN WILD-TYPE 31  8
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7                39 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                1                 8 
$`8P GAIN MUTATED`
TCGA-FF-8041 TCGA-GR-7353 TCGA-GS-A9TQ TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9U3 
       35.54        98.07        27.32        47.84        37.22        89.33 
TCGA-GS-A9U4 
       12.85 

$`8P GAIN 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        13.15        13.48 
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-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        47.38       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      116.81       196.60       150.51        36.13        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TY TCGA-GS-A9TZ 
       57.17        38.24       112.24        18.25       109.58        21.70 
TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.91         0.03         0.56 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            12.85              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            98.07            211.23 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            37.22             25.91 
[1] "12.8 - 98.1 (37.2)" "0.0 - 211.2 (25.9)"
[1] "hr=" "1.4"
D12V2, continuous
D12V3, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    5  2
  8P GAIN WILD-TYPE 21 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5    2
  8P GAIN WILD-TYPE   21   19
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               5                21
  MALE                 2                19
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  8P GAIN MUTATED                                                                                   5
  8P GAIN WILD-TYPE                                                                                35
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  8P GAIN MUTATED                          0                                  2
  8P GAIN WILD-TYPE                        3                                  2
D12V4, multiclass
                                                                                   clus
vv                                                                                  8P GAIN 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                                                                                  8P GAIN 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                                                                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
  8P GAIN MUTATED       1                         0     6
  8P GAIN WILD-TYPE    17                         1    22
D12V5, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   1                17
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   6                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"
D12V6, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    5  2
  8P GAIN WILD-TYPE  7 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5    2
  8P GAIN WILD-TYPE    7   33
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 7
  NOT HISPANIC OR LATINO               2                33
[1] 2 2
[1] FALSE

Clustering(13) Variable = 8Q GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED    7  1
  8Q GAIN WILD-TYPE 30  8
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                8                38 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                1                 8 
$`8Q GAIN MUTATED`
TCGA-FF-8041 TCGA-GR-7353 TCGA-GS-A9TQ TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TZ 
       35.54        98.07        27.32        47.84        37.22        21.70 
TCGA-GS-A9U3 TCGA-GS-A9U4 
       89.33        12.85 

$`8Q GAIN 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        13.15        13.48 
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-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        47.38       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      116.81       196.60       150.51        36.13        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TY TCGA-RQ-A68N 
       57.17        38.24       112.24        18.25       109.58        25.91 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            12.85              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            98.07            211.23 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            36.38             25.96 
[1] "12.8 - 98.1 (36.4)" "0.0 - 211.2 (26.0)"
[1] "hr=" "1.6"
D13V2, continuous
D13V3, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    5  3
  8Q GAIN WILD-TYPE 21 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5    3
  8Q GAIN WILD-TYPE   21   18
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               5                21
  MALE                 3                18
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  8Q GAIN MUTATED                                                                                   5
  8Q GAIN WILD-TYPE                                                                                35
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  8Q GAIN MUTATED                          0                                  3
  8Q GAIN WILD-TYPE                        3                                  1
D13V4, multiclass
                                                                                   clus
vv                                                                                  8Q GAIN 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                                                              3
                                                                                   clus
vv                                                                                  8Q GAIN 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                                                                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
  8Q GAIN MUTATED       1                         0     7
  8Q GAIN WILD-TYPE    17                         1    21
D13V5, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   1                17
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   7                21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    6  2
  8Q GAIN WILD-TYPE  6 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6    2
  8Q GAIN WILD-TYPE    6   33
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                 6
  NOT HISPANIC OR LATINO               2                33
[1] 2 2
[1] FALSE

Clustering(14) Variable = 9P GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    6  1
  9P GAIN WILD-TYPE 31  8
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                7                39 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                 8 
$`9P GAIN MUTATED`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-A7CQ TCGA-FF-A7CW TCGA-GS-A9TV TCGA-GS-A9TW 
       23.28        35.54         9.80        26.01        18.25        47.84 
TCGA-GS-A9TZ 
       21.70 

$`9P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         1.91        13.15        13.48         8.15 
TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       14.04        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
       22.32        10.29        12.66        31.96        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       47.38       211.23        19.56       116.81       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       98.07        36.13        42.71        43.86        57.17        27.32 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9U3 TCGA-GS-A9U4 
       38.24       112.24        37.22       109.58        89.33        12.85 
TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.91         0.03         0.56 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             9.80              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            47.84            211.23 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            23.28             31.10 
[1] "9.8 - 47.8 (23.3)"  "0.0 - 211.2 (31.1)"
[1] "hr=" "1"  
D14V2, continuous
D14V3, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    3  4
  9P GAIN WILD-TYPE 23 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    4
  9P GAIN WILD-TYPE   23   17
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               3                23
  MALE                 4                17
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  9P GAIN MUTATED                                                                                   3
  9P GAIN WILD-TYPE                                                                                37
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  9P GAIN MUTATED                          0                                  4
  9P GAIN WILD-TYPE                        3                                  0
D14V4, multiclass
                                                                                   clus
vv                                                                                  9P GAIN 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                                                              4
                                                                                   clus
vv                                                                                  9P GAIN 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                                                                0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       4                         0     3
  9P GAIN WILD-TYPE    14                         1    25
D14V5, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   4                14
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                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"
D14V6, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    3  4
  9P GAIN WILD-TYPE  9 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    4
  9P GAIN WILD-TYPE    9   31
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO               4                31
[1] 2 2
[1] FALSE

Clustering(15) Variable = 9Q GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED    6  1
  9Q GAIN WILD-TYPE 31  8
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7                39 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                 8 
$`9Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-A7CQ TCGA-FF-A7CW TCGA-GS-A9TW TCGA-GS-A9TX 
       23.28        35.54         9.80        26.01        47.84        37.22 
TCGA-GS-A9TZ 
       21.70 

$`9Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         1.91        13.15        13.48         8.15 
TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       14.04        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
       22.32        10.29        12.66        31.96        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       47.38       211.23        19.56       116.81       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       98.07        36.13        42.71        43.86        57.17        27.32 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TY TCGA-GS-A9U3 TCGA-GS-A9U4 
       38.24       112.24        18.25       109.58        89.33        12.85 
TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.91         0.03         0.56 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             9.80              0.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            47.84            211.23 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            26.01             27.35 
[1] "9.8 - 47.8 (26.0)"  "0.0 - 211.2 (27.4)"
[1] "hr=" "1.1"
D15V2, continuous
D15V3, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    2  5
  9Q GAIN WILD-TYPE 24 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2    5
  9Q GAIN WILD-TYPE   24   16
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               2                24
  MALE                 5                16
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  9Q GAIN MUTATED                                                                                   4
  9Q GAIN WILD-TYPE                                                                                36
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  9Q GAIN MUTATED                          0                                  3
  9Q GAIN WILD-TYPE                        3                                  1
D15V4, multiclass
                                                                                   clus
vv                                                                                  9Q GAIN 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                                                              3
                                                                                   clus
vv                                                                                  9Q GAIN 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                                                                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
  9Q GAIN MUTATED       4                         0     3
  9Q GAIN WILD-TYPE    14                         1    25
D15V5, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   4                14
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                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"
D15V6, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    3  4
  9Q GAIN WILD-TYPE  9 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3    4
  9Q GAIN WILD-TYPE    9   31
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO               4                31
[1] 2 2
[1] FALSE

Clustering(16) Variable = 10P GAIN MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED    4  0
  10P GAIN WILD-TYPE 33  9
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 42 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 0                  9 
$`10P GAIN MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-GR-A4D4 TCGA-GS-A9TQ 
       13.15        14.04        36.13        27.32 

$`10P GAIN 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        13.48         8.15 
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-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        47.38       211.23        19.56       116.81 
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-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       112.24        18.25        47.84        37.22       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       21.70        89.33        12.85        25.91         0.03         0.56 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             13.15               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             36.13             211.23 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            20.680             29.225 
[1] "13.2 - 36.1 (20.7)" "0.0 - 211.2 (29.2)"
[1] "hr="     "7.7e+07"
D16V2, continuous
D16V3, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    4  0
  10P GAIN WILD-TYPE 22 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4    0
  10P GAIN WILD-TYPE   22   21
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                4                 22
  MALE                  0                 21
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  10P GAIN MUTATED                                                                                   4
  10P GAIN WILD-TYPE                                                                                36
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  10P GAIN MUTATED                          0
  10P GAIN WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  10P GAIN MUTATED                                    0
  10P GAIN WILD-TYPE                                  4
D16V4, multiclass
                                                                                   clus
vv                                                                                  10P GAIN 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                                                                                  10P GAIN 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
  10P GAIN MUTATED       2                         0     2
  10P GAIN WILD-TYPE    16                         1    26
D16V5, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    2                 16
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 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"
D16V6, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    1  3
  10P GAIN WILD-TYPE 11 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1    3
  10P GAIN WILD-TYPE   11   32
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO                3                 32
[1] 2 2
[1] FALSE

Clustering(17) Variable = 10Q GAIN MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                 0  1
  10Q GAIN MUTATED    4  0
  10Q GAIN WILD-TYPE 33  9
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                 42 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 0                  9 
$`10Q GAIN MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-GS-A9TQ TCGA-GS-A9TT 
       13.15        14.04        27.32        38.24 

$`10Q GAIN 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        13.48         8.15 
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-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        47.38       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        36.13        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       57.17       112.24        18.25        47.84        37.22       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       21.70        89.33        12.85        25.91         0.03         0.56 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             13.15               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             38.24             211.23 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            20.680             29.225 
[1] "13.2 - 38.2 (20.7)" "0.0 - 211.2 (29.2)"
[1] "hr="     "7.7e+07"
D17V2, continuous
D17V3, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    3  1
  10Q GAIN WILD-TYPE 23 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    1
  10Q GAIN WILD-TYPE   23   20
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                3                 23
  MALE                  1                 20
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  10Q GAIN MUTATED                                                                                   4
  10Q GAIN WILD-TYPE                                                                                36
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  10Q GAIN MUTATED                          0
  10Q GAIN WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  10Q GAIN MUTATED                                    0
  10Q GAIN WILD-TYPE                                  4
D17V4, multiclass
                                                                                   clus
vv                                                                                  10Q GAIN 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                                                                                  10Q GAIN 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
  10Q GAIN MUTATED       2                         0     2
  10Q GAIN WILD-TYPE    16                         1    26
D17V5, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    2                 16
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 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"
D17V6, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    2  2
  10Q GAIN WILD-TYPE 10 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    2
  10Q GAIN WILD-TYPE   10   33
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                2                 33
[1] 2 2
[1] FALSE

Clustering(18) Variable = 11P GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    8  1
  11P GAIN WILD-TYPE 29  8
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                 37 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                  8 
$`11P GAIN MUTATED`
TCGA-FA-A82F TCGA-FF-8043 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TW 
       14.04        31.73        42.71        57.17        27.32        47.84 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-AAAT 
       12.85        25.91         0.56 

$`11P GAIN 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        13.15        13.48 
TCGA-FA-A7Q1 TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
        8.15        35.54        31.10        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        47.38       211.23        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GS-A9TT 
      196.60       150.51        98.07        36.13        43.86        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 
      112.24        18.25        37.22       109.58        21.70        89.33 
TCGA-RQ-A6JB 
        0.03 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.56               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             57.17             211.23 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             27.32              27.35 
[1] "0.6 - 57.2 (27.3)"  "0.0 - 211.2 (27.4)"
[1] "hr=" "1.5"
D18V2, continuous
D18V3, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    8  1
  11P GAIN WILD-TYPE 18 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      8    1
  11P GAIN WILD-TYPE   18   20
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                8                 18
  MALE                  1                 20
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  11P GAIN MUTATED                                                                                   6
  11P GAIN WILD-TYPE                                                                                34
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  11P GAIN MUTATED                          2
  11P GAIN WILD-TYPE                        1
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  11P GAIN MUTATED                                    1
  11P GAIN WILD-TYPE                                  3
D18V4, multiclass
                                                                                   clus
vv                                                                                  11P GAIN MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                6
  PRIMARY DLBCL OF THE CNS                                                                         2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               1
                                                                                   clus
vv                                                                                  11P GAIN WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 34
  PRIMARY DLBCL OF THE CNS                                                                           1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       2                         0     7
  11P GAIN WILD-TYPE    16                         1    21
D18V5, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    2                 16
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    7                 21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    5  4
  11P GAIN WILD-TYPE  7 31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5    4
  11P GAIN WILD-TYPE    7   31
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                  7
  NOT HISPANIC OR LATINO                4                 31
[1] 2 2
[1] FALSE

Clustering(19) Variable = 11Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED   11  2
  11Q GAIN WILD-TYPE 26  7
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                13                 33 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                  7 
$`11Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8043 TCGA-GR-7351 TCGA-GR-7353 
       23.28        14.04        35.54        31.73       150.51        98.07 
TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TY TCGA-GS-A9U4 TCGA-RQ-A68N 
       42.71        57.17        27.32       109.58        12.85        25.91 
TCGA-RQ-AAAT 
        0.56 

$`11Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         1.91        13.15        13.48         8.15 
TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       31.10        24.69         4.14        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
       10.29        26.01        12.66        31.96        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-A4D4 
       47.38       211.23        19.56       116.81       196.60        36.13 
TCGA-GR-A4D6 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       43.86        38.24       112.24        18.25        47.84        37.22 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-RQ-A6JB 
       21.70        89.33         0.03 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.56               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            150.51             211.23 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             31.73              26.01 
[1] "0.6 - 150.5 (31.7)" "0.0 - 211.2 (26.0)"
[1] "hr=" "1.4"
D19V2, continuous
D19V3, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED   10  3
  11Q GAIN WILD-TYPE 16 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     10    3
  11Q GAIN WILD-TYPE   16   18
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               10                 16
  MALE                  3                 18
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  11Q GAIN MUTATED                                                                                  10
  11Q GAIN WILD-TYPE                                                                                30
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  11Q GAIN MUTATED                          2
  11Q GAIN WILD-TYPE                        1
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  11Q GAIN MUTATED                                    1
  11Q GAIN WILD-TYPE                                  3
D19V4, multiclass
                                                                                   clus
vv                                                                                  11Q GAIN MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               10
  PRIMARY DLBCL OF THE CNS                                                                         2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               1
                                                                                   clus
vv                                                                                  11Q GAIN WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 30
  PRIMARY DLBCL OF THE CNS                                                                           1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 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
  11Q GAIN MUTATED       4                         0     9
  11Q GAIN WILD-TYPE    14                         1    19
D19V5, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    4                 14
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    9                 19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    5  8
  11Q GAIN WILD-TYPE  7 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5    8
  11Q GAIN WILD-TYPE    7   27
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                  7
  NOT HISPANIC OR LATINO                8                 27
[1] 2 2
[1] FALSE

Clustering(20) Variable = 12P GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    5  2
  12P GAIN WILD-TYPE 32  7
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 7                 39 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                  7 
$`12P GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A7Q1 TCGA-FF-8041 TCGA-GR-A4D5 TCGA-GS-A9TT TCGA-GS-A9TZ 
       23.28         8.15        35.54        42.71        38.24        21.70 
TCGA-RQ-AAAT 
        0.56 

$`12P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A82F 
        4.34         4.34         1.91        13.15        13.48        14.04 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       31.10        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66        31.96        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        19.56       116.81       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
      150.51        98.07        36.13        43.86        57.17        27.32 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9U3 
      112.24        18.25        47.84        37.22       109.58        89.33 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
       12.85        25.91         0.03 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.56               0.03 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             42.71             211.23 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             23.28              27.35 
[1] "0.6 - 42.7 (23.3)"  "0.0 - 211.2 (27.4)"
[1] "hr=" "2.6"
D20V2, continuous
D20V3, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    4  3
  12P GAIN WILD-TYPE 22 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      4    3
  12P GAIN WILD-TYPE   22   18
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                4                 22
  MALE                  3                 18
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  12P GAIN MUTATED                                                                                   4
  12P GAIN WILD-TYPE                                                                                36
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  12P GAIN MUTATED                          1
  12P GAIN WILD-TYPE                        2
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  12P GAIN MUTATED                                    2
  12P GAIN WILD-TYPE                                  2
D20V4, multiclass
                                                                                   clus
vv                                                                                  12P GAIN MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                4
  PRIMARY DLBCL OF THE CNS                                                                         1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               2
                                                                                   clus
vv                                                                                  12P GAIN WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 36
  PRIMARY DLBCL OF THE CNS                                                                           2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       3                         0     4
  12P GAIN WILD-TYPE    15                         1    24
D20V5, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    4                 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"
D20V6, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    3  4
  12P GAIN WILD-TYPE  9 31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3    4
  12P GAIN WILD-TYPE    9   31
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  9
  NOT HISPANIC OR LATINO                4                 31
[1] 2 2
[1] FALSE

Clustering(21) Variable = 12Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    6  3
  12Q GAIN WILD-TYPE 31  6
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 9                 37 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                  6 
$`12Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A7Q1 TCGA-FF-8041 TCGA-FF-A7CR TCGA-GR-A4D5 TCGA-GS-A9TT 
       23.28         8.15        35.54        10.29        42.71        38.24 
TCGA-GS-A9TZ TCGA-RQ-A68N TCGA-RQ-AAAT 
       21.70        25.91         0.56 

$`12Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A82F 
        4.34         4.34         1.91        13.15        13.48        14.04 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       31.10        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
        9.80        26.01        12.66        31.96        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       47.38       211.23        19.56       116.81       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TU 
       98.07        36.13        43.86        57.17        27.32       112.24 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9U3 TCGA-GS-A9U4 
       18.25        47.84        37.22       109.58        89.33        12.85 
TCGA-RQ-A6JB 
        0.03 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.56               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             42.71             211.23 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             23.28              31.10 
[1] "0.6 - 42.7 (23.3)"  "0.0 - 211.2 (31.1)"
[1] "hr=" "3.8"
D21V2, continuous
D21V3, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    4  5
  12Q GAIN WILD-TYPE 22 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4    5
  12Q GAIN WILD-TYPE   22   16
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                4                 22
  MALE                  5                 16
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  12Q GAIN MUTATED                                                                                   5
  12Q GAIN WILD-TYPE                                                                                35
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  12Q GAIN MUTATED                          2
  12Q GAIN WILD-TYPE                        1
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  12Q GAIN MUTATED                                    2
  12Q GAIN WILD-TYPE                                  2
D21V4, multiclass
                                                                                   clus
vv                                                                                  12Q GAIN MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                5
  PRIMARY DLBCL OF THE CNS                                                                         2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               2
                                                                                   clus
vv                                                                                  12Q GAIN WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 35
  PRIMARY DLBCL OF THE CNS                                                                           1
  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
  12Q GAIN MUTATED       4                         0     5
  12Q GAIN WILD-TYPE    14                         1    23
D21V5, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    4                 14
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    5                 23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    4  5
  12Q GAIN WILD-TYPE  8 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4    5
  12Q GAIN WILD-TYPE    8   30
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  8
  NOT HISPANIC OR LATINO                5                 30
[1] 2 2
[1] FALSE

Clustering(22) Variable = 13Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    4  1
  13Q GAIN WILD-TYPE 33  8
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                 41 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                  8 
$`13Q GAIN MUTATED`
TCGA-FA-A6HO TCGA-FF-8046 TCGA-FF-A7CX TCGA-GS-A9TQ TCGA-GS-A9U4 
       13.15        24.69        12.66        27.32        12.85 

$`13Q GAIN 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        13.48         8.15 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 
       14.04        35.54        31.10        31.73         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FM-8000 TCGA-G8-6324 
       22.32         9.80        10.29        26.01        31.96        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        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        36.13        42.71        43.86        57.17 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       112.24        18.25        47.84        37.22       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       21.70        89.33        25.91         0.03         0.56 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             12.66               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             27.32             211.23 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             13.15              31.73 
[1] "12.7 - 27.3 (13.2)" "0.0 - 211.2 (31.7)"
[1] "hr=" "1.8"
D22V2, continuous
D22V3, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    3  2
  13Q GAIN WILD-TYPE 23 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3    2
  13Q GAIN WILD-TYPE   23   19
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                3                 23
  MALE                  2                 19
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  13Q GAIN MUTATED                                                                                   5
  13Q GAIN WILD-TYPE                                                                                35
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  13Q GAIN MUTATED                          0
  13Q GAIN WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  13Q GAIN MUTATED                                    0
  13Q GAIN WILD-TYPE                                  4
D22V4, multiclass
                                                                                   clus
vv                                                                                  13Q GAIN 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                                                                                  13Q GAIN 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
  13Q GAIN MUTATED       3                         0     2
  13Q GAIN WILD-TYPE    15                         1    26
D22V5, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 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"
D22V6, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    2  3
  13Q GAIN WILD-TYPE 10 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2    3
  13Q GAIN WILD-TYPE   10   32
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                3                 32
[1] 2 2
[1] FALSE

Clustering(23) Variable = 16P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    5  2
  16P GAIN WILD-TYPE 32  7
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                 39 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                  7 
$`16P GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FM-8000 TCGA-GR-A4D4 TCGA-GS-A9TZ 
       23.28         8.15        14.04        31.96        36.13        21.70 
TCGA-RQ-A68N 
       25.91 

$`16P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FF-8041 
        4.34         4.34         1.91        13.15        13.48        35.54 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       31.10        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6325 
        9.80        10.29        26.01        12.66        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       47.38       211.23        19.56       116.81       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT 
       98.07        42.71        43.86        57.17        27.32        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9U3 
      112.24        18.25        47.84        37.22       109.58        89.33 
TCGA-GS-A9U4 TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85         0.03         0.56 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              8.15               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             36.13             211.23 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             23.28              31.10 
[1] "8.2 - 36.1 (23.3)"  "0.0 - 211.2 (31.1)"
[1] "hr=" "2.6"
D23V2, continuous
D23V3, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    4  3
  16P GAIN WILD-TYPE 22 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4    3
  16P GAIN WILD-TYPE   22   18
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                4                 22
  MALE                  3                 18
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  16P GAIN MUTATED                                                                                   5
  16P GAIN WILD-TYPE                                                                                35
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  16P GAIN MUTATED                          1
  16P GAIN WILD-TYPE                        2
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  16P GAIN MUTATED                                    1
  16P GAIN WILD-TYPE                                  3
D23V4, multiclass
                                                                                   clus
vv                                                                                  16P GAIN MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                5
  PRIMARY DLBCL OF THE CNS                                                                         1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               1
                                                                                   clus
vv                                                                                  16P GAIN 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                                                                 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
  16P GAIN MUTATED       3                         0     4
  16P GAIN WILD-TYPE    15                         1    24
D23V5, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    4                 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"
D23V6, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    2  5
  16P GAIN WILD-TYPE 10 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2    5
  16P GAIN WILD-TYPE   10   30
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                5                 30
[1] 2 2
[1] FALSE

Clustering(24) Variable = 16Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    4  3
  16Q GAIN WILD-TYPE 33  6
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                 39 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                  6 
$`16Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FM-8000 TCGA-G8-6909 TCGA-GS-A9TZ 
       23.28         8.15        14.04        31.96       116.81        21.70 
TCGA-RQ-A68N 
       25.91 

$`16Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FF-8041 
        4.34         4.34         1.91        13.15        13.48        35.54 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       31.10        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6325 
        9.80        10.29        26.01        12.66        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 
       47.38       211.23        19.56       196.60       150.51        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT 
       36.13        42.71        43.86        57.17        27.32        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9U3 
      112.24        18.25        47.84        37.22       109.58        89.33 
TCGA-GS-A9U4 TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85         0.03         0.56 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              8.15               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            116.81             211.23 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             23.28              31.10 
[1] "8.2 - 116.8 (23.3)" "0.0 - 211.2 (31.1)"
[1] "hr=" "3.2"
D24V2, continuous
D24V3, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3  4
  16Q GAIN WILD-TYPE 23 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3    4
  16Q GAIN WILD-TYPE   23   17
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                3                 23
  MALE                  4                 17
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  16Q GAIN MUTATED                                                                                   5
  16Q GAIN WILD-TYPE                                                                                35
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  16Q GAIN MUTATED                          1
  16Q GAIN WILD-TYPE                        2
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  16Q GAIN MUTATED                                    1
  16Q GAIN WILD-TYPE                                  3
D24V4, multiclass
                                                                                   clus
vv                                                                                  16Q GAIN MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                5
  PRIMARY DLBCL OF THE CNS                                                                         1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               1
                                                                                   clus
vv                                                                                  16Q GAIN 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                                                                 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
  16Q GAIN MUTATED       3                         0     4
  16Q GAIN WILD-TYPE    15                         1    24
D24V5, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    4                 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"
D24V6, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    2  5
  16Q GAIN WILD-TYPE 10 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2    5
  16Q GAIN WILD-TYPE   10   30
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                5                 30
[1] 2 2
[1] FALSE

Clustering(25) Variable = 17Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    2  1
  17Q GAIN WILD-TYPE 35  8
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                 43 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                  8 
$`17Q GAIN MUTATED`
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 
        8.15        14.04        35.54 

$`17Q GAIN 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        13.15        13.48 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       31.10        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66        31.96        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        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        36.13        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       27.32        38.24       112.24        18.25        47.84        37.22 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        21.70        89.33        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              8.15               0.03 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             35.54             211.23 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             14.04              27.35 
[1] "8.2 - 35.5 (14.0)"  "0.0 - 211.2 (27.4)"
[1] "hr=" "3.6"
D25V2, continuous
D25V3, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    3  0
  17Q GAIN WILD-TYPE 23 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3    0
  17Q GAIN WILD-TYPE   23   21
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                3                 23
  MALE                  0                 21
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  17Q GAIN MUTATED                                                                                   2
  17Q GAIN WILD-TYPE                                                                                38
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  17Q GAIN MUTATED                          0
  17Q GAIN WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  17Q GAIN MUTATED                                    1
  17Q GAIN WILD-TYPE                                  3
D25V4, multiclass
                                                                                   clus
vv                                                                                  17Q GAIN 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                                                                                  17Q GAIN 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
  17Q GAIN MUTATED       3                         0     0
  17Q GAIN WILD-TYPE    15                         1    28
D25V5, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    0                 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"
D25V6, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    0  3
  17Q GAIN WILD-TYPE 12 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0    3
  17Q GAIN WILD-TYPE   12   32
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                3                 32
[1] 2 2
[1] FALSE

Clustering(26) Variable = 18P GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED   13  0
  18P GAIN WILD-TYPE 24  9
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                13                 33 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 0                  9 
$`18P GAIN MUTATED`
TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-A7CQ 
       13.15        13.48        14.04        31.10        31.73         9.80 
TCGA-FF-A7CW TCGA-G8-6914 TCGA-GR-A4D6 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TW 
       26.01       196.60        43.86        38.24       112.24        47.84 
TCGA-GS-A9U3 
       89.33 

$`18P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7Q1 TCGA-FF-8041 
        4.34         4.34        23.28         1.91         8.15        35.54 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CR TCGA-FF-A7CX 
       24.69         4.14        27.35        22.32        10.29        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        47.38       211.23        19.56 
TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 
      116.81       150.51        98.07        36.13        42.71        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U4 
       27.32        18.25        37.22       109.58        21.70        12.85 
TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.91         0.03         0.56 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              9.80               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            196.60             211.23 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             31.73              25.91 
[1] "9.8 - 196.6 (31.7)" "0.0 - 211.2 (25.9)"
[1] "hr="     "3.3e+08"
D26V2, continuous
D26V3, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    8  5
  18P GAIN WILD-TYPE 18 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      8    5
  18P GAIN WILD-TYPE   18   16
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                8                 18
  MALE                  5                 16
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  18P GAIN MUTATED                                                                                  12
  18P GAIN WILD-TYPE                                                                                28
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  18P GAIN MUTATED                          0
  18P GAIN WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  18P GAIN MUTATED                                    1
  18P GAIN WILD-TYPE                                  3
D26V4, multiclass
                                                                                   clus
vv                                                                                  18P GAIN MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               12
  PRIMARY DLBCL OF THE CNS                                                                         0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               1
                                                                                   clus
vv                                                                                  18P GAIN WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 28
  PRIMARY DLBCL OF THE CNS                                                                           3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       8                         0     5
  18P GAIN WILD-TYPE    10                         1    23
D26V5, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    8                 10
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    5                 23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    4  9
  18P GAIN WILD-TYPE  8 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4    9
  18P GAIN WILD-TYPE    8   26
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  8
  NOT HISPANIC OR LATINO                9                 26
[1] 2 2
[1] FALSE

Clustering(27) Variable = 18Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED   13  1
  18Q GAIN WILD-TYPE 24  8
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                14                 32 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                  8 
$`18Q GAIN MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8043 
       23.28        13.15        13.48        14.04        31.10        31.73 
TCGA-FF-A7CQ TCGA-FF-A7CW TCGA-G8-6914 TCGA-GR-A4D6 TCGA-GS-A9TT TCGA-GS-A9TU 
        9.80        26.01       196.60        43.86        38.24       112.24 
TCGA-GS-A9TW TCGA-GS-A9U3 
       47.84        89.33 

$`18Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A7Q1 TCGA-FF-8041 TCGA-FF-8046 
        4.34         4.34         1.91         8.15        35.54        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 
        4.14        27.35        22.32        10.29        12.66        31.96 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        47.38       211.23        19.56       116.81 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TQ 
      150.51        98.07        36.13        42.71        57.17        27.32 
TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U4 TCGA-RQ-A68N 
       18.25        37.22       109.58        21.70        12.85        25.91 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              9.80               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            196.60             211.23 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            31.415             26.615 
[1] "9.8 - 196.6 (31.4)" "0.0 - 211.2 (26.6)"
[1] "hr=" "3.5"
D27V2, continuous
D27V3, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    8  6
  18Q GAIN WILD-TYPE 18 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      8    6
  18Q GAIN WILD-TYPE   18   15
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                8                 18
  MALE                  6                 15
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  18Q GAIN MUTATED                                                                                  13
  18Q GAIN WILD-TYPE                                                                                27
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  18Q GAIN MUTATED                          0
  18Q GAIN WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  18Q GAIN MUTATED                                    1
  18Q GAIN WILD-TYPE                                  3
D27V4, multiclass
                                                                                   clus
vv                                                                                  18Q GAIN MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               13
  PRIMARY DLBCL OF THE CNS                                                                         0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               1
                                                                                   clus
vv                                                                                  18Q GAIN WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 27
  PRIMARY DLBCL OF THE CNS                                                                           3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       9                         0     5
  18Q GAIN WILD-TYPE     9                         1    23
D27V5, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    9                  9
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    5                 23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    4 10
  18Q GAIN WILD-TYPE  8 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4   10
  18Q GAIN WILD-TYPE    8   25
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  8
  NOT HISPANIC OR LATINO               10                 25
[1] 2 2
[1] FALSE

Clustering(28) Variable = 19P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED    3  0
  19P GAIN WILD-TYPE 34  9
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                 43 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 0                  9 
$`19P GAIN MUTATED`
TCGA-FA-A6HO TCGA-GS-A9TT TCGA-GS-A9TY 
       13.15        38.24       109.58 

$`19P GAIN 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        13.48         8.15 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       14.04        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       31.96        41.16        51.98        47.38       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        36.13        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       43.86        57.17        27.32       112.24        18.25        47.84 
TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
       37.22        21.70        89.33        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             13.15               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            109.58             211.23 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             38.24              27.32 
[1] "13.2 - 109.6 (38.2)" "0.0 - 211.2 (27.3)" 
[1] "hr="     "7.4e+07"
D28V2, continuous
D28V3, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    2  1
  19P GAIN WILD-TYPE 24 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2    1
  19P GAIN WILD-TYPE   24   20
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                2                 24
  MALE                  1                 20
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  19P GAIN MUTATED                                                                                   3
  19P GAIN WILD-TYPE                                                                                37
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  19P GAIN MUTATED                          0
  19P GAIN WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  19P GAIN MUTATED                                    0
  19P GAIN WILD-TYPE                                  4
D28V4, multiclass
                                                                                   clus
vv                                                                                  19P GAIN 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                                                                                  19P GAIN 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
  19P GAIN MUTATED       1                         0     2
  19P GAIN WILD-TYPE    17                         1    26
D28V5, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    1                 17
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 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"
D28V6, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    2  1
  19P GAIN WILD-TYPE 10 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2    1
  19P GAIN WILD-TYPE   10   34
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                1                 34
[1] 2 2
[1] FALSE

Clustering(29) Variable = 19Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED    3  0
  19Q GAIN WILD-TYPE 34  9
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                 43 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 0                  9 
$`19Q GAIN MUTATED`
TCGA-FA-A6HO TCGA-GS-A9TT TCGA-GS-A9TY 
       13.15        38.24       109.58 

$`19Q GAIN 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        13.48         8.15 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       14.04        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       31.96        41.16        51.98        47.38       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        36.13        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       43.86        57.17        27.32       112.24        18.25        47.84 
TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
       37.22        21.70        89.33        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             13.15               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            109.58             211.23 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             38.24              27.32 
[1] "13.2 - 109.6 (38.2)" "0.0 - 211.2 (27.3)" 
[1] "hr="     "7.4e+07"
D29V2, continuous
D29V3, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    2  1
  19Q GAIN WILD-TYPE 24 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2    1
  19Q GAIN WILD-TYPE   24   20
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                2                 24
  MALE                  1                 20
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  19Q GAIN MUTATED                                                                                   3
  19Q GAIN WILD-TYPE                                                                                37
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  19Q GAIN MUTATED                          0
  19Q GAIN WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  19Q GAIN MUTATED                                    0
  19Q GAIN WILD-TYPE                                  4
D29V4, multiclass
                                                                                   clus
vv                                                                                  19Q GAIN 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                                                                                  19Q GAIN 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
  19Q GAIN MUTATED       1                         0     2
  19Q GAIN WILD-TYPE    17                         1    26
D29V5, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    1                 17
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 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"
D29V6, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    2  1
  19Q GAIN WILD-TYPE 10 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2    1
  19Q GAIN WILD-TYPE   10   34
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                1                 34
[1] 2 2
[1] FALSE

Clustering(30) Variable = 20P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED    4  1
  20P GAIN WILD-TYPE 33  8
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 5                 41 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 1                  8 
$`20P GAIN MUTATED`
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8043 TCGA-GS-A9TY TCGA-GS-A9U4 
       14.04        35.54        31.73       109.58        12.85 

$`20P GAIN 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        13.15        13.48 
TCGA-FA-A7Q1 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
        8.15        31.10        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66        31.96        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        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        36.13        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       27.32        38.24       112.24        18.25        47.84        37.22 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       21.70        89.33        25.91         0.03         0.56 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             12.85               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            109.58             211.23 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             31.73              27.32 
[1] "12.8 - 109.6 (31.7)" "0.0 - 211.2 (27.3)" 
[1] "hr=" "1.3"
D30V2, continuous
D30V3, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    5  0
  20P GAIN WILD-TYPE 21 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      5    0
  20P GAIN WILD-TYPE   21   21
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                5                 21
  MALE                  0                 21
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  20P GAIN MUTATED                                                                                   4
  20P GAIN WILD-TYPE                                                                                36
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  20P GAIN MUTATED                          0
  20P GAIN WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  20P GAIN MUTATED                                    1
  20P GAIN WILD-TYPE                                  3
D30V4, multiclass
                                                                                   clus
vv                                                                                  20P GAIN 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                                                                                  20P GAIN 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                                                                 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
  20P GAIN MUTATED       3                         0     2
  20P GAIN WILD-TYPE    15                         1    26
D30V5, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 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"
D30V6, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    2  3
  20P GAIN WILD-TYPE 10 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2    3
  20P GAIN WILD-TYPE   10   32
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                3                 32
[1] 2 2
[1] FALSE

Clustering(31) Variable = 20Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED    3  1
  20Q GAIN WILD-TYPE 34  8
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 4                 42 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 1                  8 
$`20Q GAIN MUTATED`
TCGA-FA-A82F TCGA-FF-8041 TCGA-GS-A9TY TCGA-GS-A9U4 
       14.04        35.54       109.58        12.85 

$`20Q GAIN 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        13.15        13.48 
TCGA-FA-A7Q1 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
        8.15        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-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        47.38       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        36.13        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       57.17        27.32        38.24       112.24        18.25        47.84 
TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       37.22        21.70        89.33        25.91         0.03         0.56 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             12.85               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            109.58             211.23 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            24.790             27.335 
[1] "12.8 - 109.6 (24.8)" "0.0 - 211.2 (27.3)" 
[1] "hr=" "1.8"
D31V2, continuous
D31V3, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    4  0
  20Q GAIN WILD-TYPE 22 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4    0
  20Q GAIN WILD-TYPE   22   21
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                4                 22
  MALE                  0                 21
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  20Q GAIN MUTATED                                                                                   3
  20Q GAIN WILD-TYPE                                                                                37
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  20Q GAIN MUTATED                          0
  20Q GAIN WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  20Q GAIN MUTATED                                    1
  20Q GAIN WILD-TYPE                                  3
D31V4, multiclass
                                                                                   clus
vv                                                                                  20Q GAIN 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                                                                                  20Q GAIN 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
  20Q GAIN MUTATED       2                         0     2
  20Q GAIN WILD-TYPE    16                         1    26
D31V5, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    2                 16
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 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"
D31V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    2  2
  20Q GAIN WILD-TYPE 10 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2    2
  20Q GAIN WILD-TYPE   10   33
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                2                 33
[1] 2 2
[1] FALSE

Clustering(32) Variable = 21Q GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    8  2
  21Q GAIN WILD-TYPE 29  7
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                 36 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                  7 
$`21Q GAIN MUTATED`
TCGA-FA-A4BB TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8043 TCGA-G8-6909 TCGA-GR-7351 
        4.34        14.04        35.54        31.73       116.81       150.51 
TCGA-GR-7353 TCGA-GS-A9TW TCGA-GS-A9TY TCGA-GS-A9U4 
       98.07        47.84       109.58        12.85 

$`21Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34        23.28         1.91        13.15        13.48         8.15 
TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       31.10        24.69         4.14        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
       10.29        26.01        12.66        31.96        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-A4D4 TCGA-GR-A4D5 
       47.38       211.23        19.56       196.60        36.13        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV 
       43.86        57.17        27.32        38.24       112.24        18.25 
TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       37.22        21.70        89.33        25.91         0.03         0.56 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              4.34               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            150.51             211.23 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             41.69              25.96 
[1] "4.3 - 150.5 (41.7)" "0.0 - 211.2 (26.0)"
[1] "hr=" "1.2"
D32V2, continuous
D32V3, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    7  3
  21Q GAIN WILD-TYPE 19 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      7    3
  21Q GAIN WILD-TYPE   19   18
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                7                 19
  MALE                  3                 18
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  21Q GAIN MUTATED                                                                                   8
  21Q GAIN WILD-TYPE                                                                                32
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  21Q GAIN MUTATED                          0
  21Q GAIN WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  21Q GAIN MUTATED                                    2
  21Q GAIN WILD-TYPE                                  2
D32V4, multiclass
                                                                                   clus
vv                                                                                  21Q GAIN MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                8
  PRIMARY DLBCL OF THE CNS                                                                         0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               2
                                                                                   clus
vv                                                                                  21Q GAIN 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                                                                 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
  21Q GAIN MUTATED       3                         0     7
  21Q GAIN WILD-TYPE    15                         1    21
D32V5, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    7                 21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    3  7
  21Q GAIN WILD-TYPE  9 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    7
  21Q GAIN WILD-TYPE    9   28
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  9
  NOT HISPANIC OR LATINO                7                 28
[1] 2 2
[1] FALSE

Clustering(33) Variable = XP GAIN MUTATION ANALYSIS
D33V1, survival
                   sevent
clus2                0  1
  XP GAIN MUTATED    5  1
  XP GAIN WILD-TYPE 32  8
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                6                40 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                1                 8 
$`XP GAIN MUTATED`
TCGA-FA-A4XK TCGA-FF-A7CW TCGA-GS-A9TW TCGA-GS-A9TY TCGA-RQ-A68N TCGA-RQ-AAAT 
       23.28        26.01        47.84       109.58        25.91         0.56 

$`XP GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         1.91        13.15        13.48         8.15 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       14.04        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 
       27.35        22.32         9.80        10.29        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        47.38       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        36.13        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TX 
       57.17        27.32        38.24       112.24        18.25        37.22 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB 
       21.70        89.33        12.85         0.03 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.56              0.03 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           109.58            211.23 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           25.960            29.225 
[1] "0.6 - 109.6 (26.0)" "0.0 - 211.2 (29.2)"
[1] "hr=" "1"  
D33V2, continuous
D33V3, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    3  3
  XP GAIN WILD-TYPE 23 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      3    3
  XP GAIN WILD-TYPE   23   18
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE               3                23
  MALE                 3                18
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  XP GAIN MUTATED                                                                                   3
  XP GAIN WILD-TYPE                                                                                37
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  XP GAIN MUTATED                          2                                  1
  XP GAIN WILD-TYPE                        1                                  3
D33V4, multiclass
                                                                                   clus
vv                                                                                  XP GAIN 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                                                              1
                                                                                   clus
vv                                                                                  XP GAIN WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                37
  PRIMARY DLBCL OF THE CNS                                                                          1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED       2                         0     4
  XP GAIN WILD-TYPE    16                         1    24
D33V5, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   2                16
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   4                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"
D33V6, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    4  2
  XP GAIN WILD-TYPE  8 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      4    2
  XP GAIN WILD-TYPE    8   33
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 8
  NOT HISPANIC OR LATINO               2                33
[1] 2 2
[1] FALSE

Clustering(34) Variable = XQ GAIN MUTATION ANALYSIS
D34V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED    5  1
  XQ GAIN WILD-TYPE 32  8
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6                40 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                 8 
$`XQ GAIN MUTATED`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-A7CW TCGA-GS-A9U3 TCGA-RQ-A68N TCGA-RQ-AAAT 
       23.28        35.54        26.01        89.33        25.91         0.56 

$`XQ GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         1.91        13.15        13.48         8.15 
TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       14.04        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
       22.32         9.80        10.29        12.66        31.96        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        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        36.13        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       27.32        38.24       112.24        18.25        47.84        37.22 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U4 TCGA-RQ-A6JB 
      109.58        21.70        12.85         0.03 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.56              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            89.33            211.23 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           25.960            29.225 
[1] "0.6 - 89.3 (26.0)"  "0.0 - 211.2 (29.2)"
[1] "hr=" "1.1"
D34V2, continuous
D34V3, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    3  3
  XQ GAIN WILD-TYPE 23 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3    3
  XQ GAIN WILD-TYPE   23   18
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               3                23
  MALE                 3                18
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  XQ GAIN MUTATED                                                                                   3
  XQ GAIN WILD-TYPE                                                                                37
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  XQ GAIN MUTATED                          2                                  1
  XQ GAIN WILD-TYPE                        1                                  3
D34V4, multiclass
                                                                                   clus
vv                                                                                  XQ GAIN 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                                                              1
                                                                                   clus
vv                                                                                  XQ GAIN WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                37
  PRIMARY DLBCL OF THE CNS                                                                          1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       3                         0     3
  XQ GAIN WILD-TYPE    15                         1    25
D34V5, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                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"
D34V6, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    3  3
  XQ GAIN WILD-TYPE  9 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3    3
  XQ GAIN WILD-TYPE    9   32
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO               3                32
[1] 2 2
[1] FALSE

Clustering(35) Variable = 1P LOSS MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED    3  0
  1P LOSS WILD-TYPE 34  9
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                43 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                0                 9 
$`1P LOSS MUTATED`
TCGA-FA-A6HO TCGA-G8-6325 TCGA-RQ-A68N 
       13.15        51.98        25.91 

$`1P LOSS 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        13.48         8.15 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       14.04        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       31.96        41.16        47.38       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        36.13        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       57.17        27.32        38.24       112.24        18.25        47.84 
TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB 
       37.22       109.58        21.70        89.33        12.85         0.03 
TCGA-RQ-AAAT 
        0.56 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            13.15              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            51.98            211.23 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            25.91             27.35 
[1] "13.2 - 52.0 (25.9)" "0.0 - 211.2 (27.4)"
[1] "hr="     "7.4e+07"
D35V2, continuous
D35V3, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1  2
  1P LOSS WILD-TYPE 25 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    2
  1P LOSS WILD-TYPE   25   19
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               1                25
  MALE                 2                19
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  1P LOSS MUTATED                                                                                   2
  1P LOSS WILD-TYPE                                                                                38
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  1P LOSS MUTATED                          1                                  0
  1P LOSS WILD-TYPE                        2                                  4
D35V4, multiclass
                                                                                   clus
vv                                                                                  1P LOSS 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                                                                                  1P LOSS 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
  1P LOSS MUTATED       1                         0     2
  1P LOSS WILD-TYPE    17                         1    26
D35V5, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   1                17
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   2                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"
D35V6, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1  2
  1P LOSS WILD-TYPE 11 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    2
  1P LOSS WILD-TYPE   11   33
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               2                33
[1] 2 2
[1] FALSE

Clustering(36) Variable = 3P LOSS MUTATION ANALYSIS
D36V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    4  0
  3P LOSS WILD-TYPE 33  9
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                4                42 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                0                 9 
$`3P LOSS MUTATED`
TCGA-G8-6325 TCGA-GS-A9TQ TCGA-GS-A9TZ TCGA-RQ-AAAT 
       51.98        27.32        21.70         0.56 

$`3P LOSS 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        13.15        13.48 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
        8.15        14.04        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       12.66        31.96        41.16        47.38       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        36.13        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       43.86        57.17        38.24       112.24        18.25        47.84 
TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
       37.22       109.58        89.33        12.85        25.91         0.03 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.56              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            51.98            211.23 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           24.510            29.225 
[1] "0.6 - 52.0 (24.5)"  "0.0 - 211.2 (29.2)"
[1] "hr="     "7.5e+07"
D36V2, continuous
D36V3, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    3  2
  3P LOSS WILD-TYPE 23 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3    2
  3P LOSS WILD-TYPE   23   19
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               3                23
  MALE                 2                19
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  3P LOSS MUTATED                                                                                   3
  3P LOSS WILD-TYPE                                                                                37
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  3P LOSS MUTATED                          1                                  1
  3P LOSS WILD-TYPE                        2                                  3
D36V4, multiclass
                                                                                   clus
vv                                                                                  3P LOSS 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                                                                                  3P LOSS 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                                                                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
  3P LOSS MUTATED       0                         0     5
  3P LOSS WILD-TYPE    18                         1    23
D36V5, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   0                18
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   5                23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    3  2
  3P LOSS WILD-TYPE  9 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3    2
  3P LOSS WILD-TYPE    9   33
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO               2                33
[1] 2 2
[1] FALSE

Clustering(37) Variable = 3Q LOSS MUTATION ANALYSIS
D37V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    4  0
  3Q LOSS WILD-TYPE 33  9
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4                42 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                0                 9 
$`3Q LOSS MUTATED`
TCGA-G8-6325 TCGA-GS-A9TQ TCGA-GS-A9TZ TCGA-RQ-AAAT 
       51.98        27.32        21.70         0.56 

$`3Q LOSS 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        13.15        13.48 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
        8.15        14.04        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       12.66        31.96        41.16        47.38       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        36.13        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       43.86        57.17        38.24       112.24        18.25        47.84 
TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
       37.22       109.58        89.33        12.85        25.91         0.03 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.56              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            51.98            211.23 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           24.510            29.225 
[1] "0.6 - 52.0 (24.5)"  "0.0 - 211.2 (29.2)"
[1] "hr="     "7.5e+07"
D37V2, continuous
D37V3, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    2  2
  3Q LOSS WILD-TYPE 24 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    2
  3Q LOSS WILD-TYPE   24   19
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               2                24
  MALE                 2                19
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  3Q LOSS MUTATED                                                                                   2
  3Q LOSS WILD-TYPE                                                                                38
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  3Q LOSS MUTATED                          1                                  1
  3Q LOSS WILD-TYPE                        2                                  3
D37V4, multiclass
                                                                                   clus
vv                                                                                  3Q LOSS 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                                                                                  3Q LOSS 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
  3Q LOSS MUTATED       0                         0     4
  3Q LOSS WILD-TYPE    18                         1    24
D37V5, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   0                18
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   4                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"
D37V6, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    3  1
  3Q LOSS WILD-TYPE  9 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    1
  3Q LOSS WILD-TYPE    9   34
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO               1                34
[1] 2 2
[1] FALSE

Clustering(38) Variable = 4P LOSS MUTATION ANALYSIS
D38V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    2  0
  4P LOSS WILD-TYPE 35  9
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                44 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                0                 9 
$`4P LOSS MUTATED`
TCGA-FA-A6HO TCGA-GS-A9TQ 
       13.15        27.32 

$`4P LOSS 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        13.48         8.15 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       14.04        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       31.96        41.16        51.98        47.38       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        36.13        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       43.86        57.17        38.24       112.24        18.25        47.84 
TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N 
       37.22       109.58        21.70        89.33        12.85        25.91 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            13.15              0.03 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            27.32            211.23 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           20.235            29.225 
[1] "13.2 - 27.3 (20.2)" "0.0 - 211.2 (29.2)"
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
D38V2, continuous
D38V3, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    3  0
  4P LOSS WILD-TYPE 23 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3    0
  4P LOSS WILD-TYPE   23   21
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               3                23
  MALE                 0                21
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  4P LOSS MUTATED                                                                                   3
  4P LOSS WILD-TYPE                                                                                37
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  4P LOSS MUTATED                          0                                  0
  4P LOSS WILD-TYPE                        3                                  4
D38V4, multiclass
                                                                                   clus
vv                                                                                  4P LOSS 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                                                                                  4P LOSS 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
  4P LOSS MUTATED       1                         0     2
  4P LOSS WILD-TYPE    17                         1    26
D38V5, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   1                17
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   2                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"
D38V6, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    1  2
  4P LOSS WILD-TYPE 11 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1    2
  4P LOSS WILD-TYPE   11   33
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               2                33
[1] 2 2
[1] FALSE

Clustering(39) Variable = 4Q LOSS MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    3  0
  4Q LOSS WILD-TYPE 34  9
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                3                43 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                0                 9 
$`4Q LOSS MUTATED`
TCGA-FF-8043 TCGA-FF-8047 TCGA-GS-A9TQ 
       31.73         4.14        27.32 

$`4Q LOSS 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        13.15        13.48 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8061 
        8.15        14.04        35.54        31.10        24.69        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        47.38       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        36.13        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       57.17        38.24       112.24        18.25        47.84        37.22 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        21.70        89.33        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             4.14              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            31.73            211.23 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            27.32             27.35 
[1] "4.1 - 31.7 (27.3)"  "0.0 - 211.2 (27.4)"
[1] "hr="     "2.7e+07"
D39V2, continuous
D39V3, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    4  0
  4Q LOSS WILD-TYPE 22 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      4    0
  4Q LOSS WILD-TYPE   22   21
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               4                22
  MALE                 0                21
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  4Q LOSS MUTATED                                                                                   4
  4Q LOSS WILD-TYPE                                                                                36
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  4Q LOSS MUTATED                          0                                  0
  4Q LOSS WILD-TYPE                        3                                  4
D39V4, multiclass
                                                                                   clus
vv                                                                                  4Q LOSS 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                                                                                  4Q LOSS 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
  4Q LOSS MUTATED       2                         0     2
  4Q LOSS WILD-TYPE    16                         1    26
D39V5, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   2                16
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   2                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"
D39V6, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    1  3
  4Q LOSS WILD-TYPE 11 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1    3
  4Q LOSS WILD-TYPE   11   32
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               3                32
[1] 2 2
[1] FALSE

Clustering(40) Variable = 6Q LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED    5  2
  6Q LOSS WILD-TYPE 32  7
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7                39 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                2                 7 
$`6Q LOSS MUTATED`
TCGA-FF-A7CX TCGA-G8-6906 TCGA-GR-A4D5 TCGA-GS-A9TY TCGA-GS-A9U4 TCGA-RQ-A68N 
       12.66       211.23        42.71       109.58        12.85        25.91 
TCGA-RQ-AAAT 
        0.56 

$`6Q LOSS 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        13.15        13.48 
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-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6907 TCGA-G8-6909 
       31.96        41.16        51.98        47.38        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 
      196.60       150.51        98.07        36.13        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       27.32        38.24       112.24        18.25        47.84        37.22 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-RQ-A6JB 
       21.70        89.33         0.03 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.56              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           211.23            196.60 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            25.91             27.35 
[1] "0.6 - 211.2 (25.9)" "0.0 - 196.6 (27.4)"
[1] "hr=" "1.4"
D40V2, continuous
D40V3, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    4  3
  6Q LOSS WILD-TYPE 22 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4    3
  6Q LOSS WILD-TYPE   22   18
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               4                22
  MALE                 3                18
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  6Q LOSS MUTATED                                                                                   5
  6Q LOSS WILD-TYPE                                                                                35
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  6Q LOSS MUTATED                          2                                  0
  6Q LOSS WILD-TYPE                        1                                  4
D40V4, multiclass
                                                                                   clus
vv                                                                                  6Q LOSS MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               5
  PRIMARY DLBCL OF THE CNS                                                                        2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              0
                                                                                   clus
vv                                                                                  6Q LOSS WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                35
  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
  6Q LOSS MUTATED       1                         0     6
  6Q LOSS WILD-TYPE    17                         1    22
D40V5, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   1                17
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   6                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"
D40V6, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    4  3
  6Q LOSS WILD-TYPE  8 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4    3
  6Q LOSS WILD-TYPE    8   32
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 8
  NOT HISPANIC OR LATINO               3                32
[1] 2 2
[1] FALSE

Clustering(41) Variable = 8P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    6  1
  8P LOSS WILD-TYPE 31  8
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                7                39 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                 8 
$`8P LOSS MUTATED`
TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FF-8047 TCGA-GR-A4D6 TCGA-GS-A9TY TCGA-GS-A9TZ 
       13.15         8.15         4.14        43.86       109.58        21.70 
TCGA-RQ-A68N 
       25.91 

$`8P LOSS WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A82F 
        4.34         4.34        23.28         1.91        13.48        14.04 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.10        31.73        24.69        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66        31.96        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        19.56       116.81       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TQ 
      150.51        98.07        36.13        42.71        57.17        27.32 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9U3 
       38.24       112.24        18.25        47.84        37.22        89.33 
TCGA-GS-A9U4 TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85         0.03         0.56 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             4.14              0.03 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           109.58            211.23 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             21.7              31.1 
[1] "4.1 - 109.6 (21.7)" "0.0 - 211.2 (31.1)"
[1] "hr=" "1.1"
D41V2, continuous
D41V3, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    6  2
  8P LOSS WILD-TYPE 20 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      6    2
  8P LOSS WILD-TYPE   20   19
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               6                20
  MALE                 2                19
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  8P LOSS MUTATED                                                                                   6
  8P LOSS WILD-TYPE                                                                                34
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  8P LOSS MUTATED                          1                                  1
  8P LOSS WILD-TYPE                        2                                  3
D41V4, multiclass
                                                                                   clus
vv                                                                                  8P LOSS 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                                                              1
                                                                                   clus
vv                                                                                  8P LOSS WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                34
  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
  8P LOSS MUTATED       4                         0     4
  8P LOSS WILD-TYPE    14                         1    24
D41V5, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   4                14
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   4                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"
D41V6, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    3  5
  8P LOSS WILD-TYPE  9 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3    5
  8P LOSS WILD-TYPE    9   30
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO               5                30
[1] 2 2
[1] FALSE

Clustering(42) Variable = 8Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    3  0
  8Q LOSS WILD-TYPE 34  9
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3                43 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                0                 9 
$`8Q LOSS MUTATED`
TCGA-FA-A6HO TCGA-GS-A9TY TCGA-RQ-A68N 
       13.15       109.58        25.91 

$`8Q LOSS 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        13.48         8.15 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       14.04        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       31.96        41.16        51.98        47.38       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        36.13        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV 
       43.86        57.17        27.32        38.24       112.24        18.25 
TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB 
       47.84        37.22        21.70        89.33        12.85         0.03 
TCGA-RQ-AAAT 
        0.56 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            13.15              0.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           109.58            211.23 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            25.91             27.35 
[1] "13.2 - 109.6 (25.9)" "0.0 - 211.2 (27.4)" 
[1] "hr="     "7.4e+07"
D42V2, continuous
D42V3, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    3  1
  8Q LOSS WILD-TYPE 23 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3    1
  8Q LOSS WILD-TYPE   23   20
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               3                23
  MALE                 1                20
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  8Q LOSS MUTATED                                                                                   3
  8Q LOSS WILD-TYPE                                                                                37
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  8Q LOSS MUTATED                          1                                  0
  8Q LOSS WILD-TYPE                        2                                  4
D42V4, multiclass
                                                                                   clus
vv                                                                                  8Q LOSS 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                                                                                  8Q LOSS 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
  8Q LOSS MUTATED       1                         0     3
  8Q LOSS WILD-TYPE    17                         1    25
D42V5, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   1                17
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                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"
D42V6, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    2  2
  8Q LOSS WILD-TYPE 10 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    2
  8Q LOSS WILD-TYPE   10   33
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO               2                33
[1] 2 2
[1] FALSE

Clustering(43) Variable = 13Q LOSS MUTATION ANALYSIS
D43V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    3  0
  13Q LOSS WILD-TYPE 34  9
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 3                 43 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 0                  9 
$`13Q LOSS MUTATED`
TCGA-GR-A4D4 TCGA-GS-A9TZ TCGA-RQ-AAAT 
       36.13        21.70         0.56 

$`13Q LOSS 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        13.15        13.48 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
        8.15        14.04        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       12.66        31.96        41.16        51.98        47.38       211.23 
TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D5 
       19.56       116.81       196.60       150.51        98.07        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV 
       43.86        57.17        27.32        38.24       112.24        18.25 
TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N 
       47.84        37.22       109.58        89.33        12.85        25.91 
TCGA-RQ-A6JB 
        0.03 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.56               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             36.13             211.23 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             21.70              27.35 
[1] "0.6 - 36.1 (21.7)"  "0.0 - 211.2 (27.4)"
[1] "hr="     "2.6e+07"
D43V2, continuous
D43V3, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    2  1
  13Q LOSS WILD-TYPE 24 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2    1
  13Q LOSS WILD-TYPE   24   20
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                2                 24
  MALE                  1                 20
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  13Q LOSS MUTATED                                                                                   1
  13Q LOSS WILD-TYPE                                                                                39
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  13Q LOSS MUTATED                          1
  13Q LOSS WILD-TYPE                        2
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  13Q LOSS MUTATED                                    1
  13Q LOSS WILD-TYPE                                  3
D43V4, multiclass
                                                                                   clus
vv                                                                                  13Q LOSS MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                1
  PRIMARY DLBCL OF THE CNS                                                                         1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               1
                                                                                   clus
vv                                                                                  13Q LOSS 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
  13Q LOSS MUTATED       0                         0     3
  13Q LOSS WILD-TYPE    18                         1    25
D43V5, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    0                 18
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                 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"
D43V6, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    2  1
  13Q LOSS WILD-TYPE 10 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2    1
  13Q LOSS WILD-TYPE   10   34
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                1                 34
[1] 2 2
[1] FALSE

Clustering(44) Variable = 15Q LOSS MUTATION ANALYSIS
D44V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    6  0
  15Q LOSS WILD-TYPE 31  9
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                 40 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 0                  9 
$`15Q LOSS MUTATED`
TCGA-FA-A6HO TCGA-FF-8043 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GS-A9TQ 
       13.15        31.73        98.07        36.13        43.86        27.32 

$`15Q LOSS 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        13.48         8.15 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       14.04        35.54        31.10        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        47.38       211.23        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU 
      196.60       150.51        42.71        57.17        38.24       112.24 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 
       18.25        47.84        37.22       109.58        21.70        89.33 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85        25.91         0.03         0.56 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             13.15               0.03 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             98.07             211.23 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             33.93              25.96 
[1] "13.2 - 98.1 (33.9)" "0.0 - 211.2 (26.0)"
[1] "hr="     "2.3e+08"
D44V2, continuous
D44V3, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    6  1
  15Q LOSS WILD-TYPE 20 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      6    1
  15Q LOSS WILD-TYPE   20   20
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                6                 20
  MALE                  1                 20
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  15Q LOSS MUTATED                                                                                   7
  15Q LOSS WILD-TYPE                                                                                33
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  15Q LOSS MUTATED                          0
  15Q LOSS WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  15Q LOSS MUTATED                                    0
  15Q LOSS WILD-TYPE                                  4
D44V4, multiclass
                                                                                   clus
vv                                                                                  15Q LOSS 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                                                                                  15Q LOSS WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 33
  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
  15Q LOSS MUTATED       3                         0     4
  15Q LOSS WILD-TYPE    15                         1    24
D44V5, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    4                 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"
D44V6, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    1  6
  15Q LOSS WILD-TYPE 11 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    6
  15Q LOSS WILD-TYPE   11   29
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO                6                 29
[1] 2 2
[1] FALSE

Clustering(45) Variable = 16Q LOSS MUTATION ANALYSIS
D45V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    4  0
  16Q LOSS WILD-TYPE 33  9
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 42 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 0                  9 
$`16Q LOSS MUTATED`
TCGA-FA-A6HO TCGA-FF-8043 TCGA-FF-8047 TCGA-GR-A4D4 
       13.15        31.73         4.14        36.13 

$`16Q LOSS 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        13.48         8.15 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 
       14.04        35.54        31.10        24.69        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66        31.96        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        19.56       116.81       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
      150.51        98.07        42.71        43.86        57.17        27.32 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       112.24        18.25        47.84        37.22       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       21.70        89.33        12.85        25.91         0.03         0.56 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              4.14               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             36.13             211.23 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            22.440             27.335 
[1] "4.1 - 36.1 (22.4)"  "0.0 - 211.2 (27.3)"
[1] "hr="     "7.5e+07"
D45V2, continuous
D45V3, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    4  0
  16Q LOSS WILD-TYPE 22 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4    0
  16Q LOSS WILD-TYPE   22   21
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                4                 22
  MALE                  0                 21
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  16Q LOSS MUTATED                                                                                   4
  16Q LOSS WILD-TYPE                                                                                36
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  16Q LOSS MUTATED                          0
  16Q LOSS WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  16Q LOSS MUTATED                                    0
  16Q LOSS WILD-TYPE                                  4
D45V4, multiclass
                                                                                   clus
vv                                                                                  16Q LOSS 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                                                                                  16Q LOSS 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
  16Q LOSS MUTATED       3                         0     1
  16Q LOSS WILD-TYPE    15                         1    27
D45V5, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    1                 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"
D45V6, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    0  4
  16Q LOSS WILD-TYPE 12 31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      0    4
  16Q LOSS WILD-TYPE   12   31
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                4                 31
[1] 2 2
[1] FALSE

Clustering(46) Variable = 17P LOSS MUTATION ANALYSIS
D46V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED    9  0
  17P LOSS WILD-TYPE 28  9
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 9                 37 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 0                  9 
$`17P LOSS MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-GR-A4D4 TCGA-GS-A9TQ TCGA-GS-A9TW TCGA-GS-A9TY 
       13.15        14.04        36.13        27.32        47.84       109.58 
TCGA-GS-A9TZ TCGA-RQ-A68N TCGA-RQ-AAAT 
       21.70        25.91         0.56 

$`17P LOSS 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        13.48         8.15 
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-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        47.38       211.23        19.56       116.81 
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-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9U3 TCGA-GS-A9U4 
       38.24       112.24        18.25        37.22        89.33        12.85 
TCGA-RQ-A6JB 
        0.03 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.56               0.03 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            109.58             211.23 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             25.91              31.10 
[1] "0.6 - 109.6 (25.9)" "0.0 - 211.2 (31.1)"
[1] "hr="     "2.5e+08"
D46V2, continuous
D46V3, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    7  2
  17P LOSS WILD-TYPE 19 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      7    2
  17P LOSS WILD-TYPE   19   19
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                7                 19
  MALE                  2                 19
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  17P LOSS MUTATED                                                                                   5
  17P LOSS WILD-TYPE                                                                                35
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  17P LOSS MUTATED                          2
  17P LOSS WILD-TYPE                        1
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  17P LOSS MUTATED                                    2
  17P LOSS WILD-TYPE                                  2
D46V4, multiclass
                                                                                   clus
vv                                                                                  17P LOSS MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                5
  PRIMARY DLBCL OF THE CNS                                                                         2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               2
                                                                                   clus
vv                                                                                  17P LOSS WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 35
  PRIMARY DLBCL OF THE CNS                                                                           1
  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
  17P LOSS MUTATED       2                         0     7
  17P LOSS WILD-TYPE    16                         1    21
D46V5, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    2                 16
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    7                 21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    6  3
  17P LOSS WILD-TYPE  6 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      6    3
  17P LOSS WILD-TYPE    6   32
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  6
  NOT HISPANIC OR LATINO                3                 32
[1] 2 2
[1] FALSE

Clustering(47) Variable = 17Q LOSS MUTATION ANALYSIS
D47V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    4  0
  17Q LOSS WILD-TYPE 33  9
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                 42 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 0                  9 
$`17Q LOSS MUTATED`
TCGA-GS-A9TQ TCGA-GS-A9TZ TCGA-RQ-A68N TCGA-RQ-AAAT 
       27.32        21.70        25.91         0.56 

$`17Q LOSS 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        13.15        13.48 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
        8.15        14.04        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       12.66        31.96        41.16        51.98        47.38       211.23 
TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 
       19.56       116.81       196.60       150.51        98.07        36.13 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV 
       42.71        43.86        57.17        38.24       112.24        18.25 
TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB 
       47.84        37.22       109.58        89.33        12.85         0.03 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.56               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             27.32             211.23 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            23.805             31.415 
[1] "0.6 - 27.3 (23.8)"  "0.0 - 211.2 (31.4)"
[1] "hr="     "7.5e+07"
D47V2, continuous
D47V3, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    2  2
  17Q LOSS WILD-TYPE 24 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    2
  17Q LOSS WILD-TYPE   24   19
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                2                 24
  MALE                  2                 19
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  17Q LOSS MUTATED                                                                                   1
  17Q LOSS WILD-TYPE                                                                                39
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  17Q LOSS MUTATED                          2
  17Q LOSS WILD-TYPE                        1
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  17Q LOSS MUTATED                                    1
  17Q LOSS WILD-TYPE                                  3
D47V4, multiclass
                                                                                   clus
vv                                                                                  17Q LOSS MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                1
  PRIMARY DLBCL OF THE CNS                                                                         2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                               1
                                                                                   clus
vv                                                                                  17Q LOSS WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 39
  PRIMARY DLBCL OF THE CNS                                                                           1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       0                         0     4
  17Q LOSS WILD-TYPE    18                         1    24
D47V5, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                 18
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    4                 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"
D47V6, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    4  0
  17Q LOSS WILD-TYPE  8 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    0
  17Q LOSS WILD-TYPE    8   35
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  8
  NOT HISPANIC OR LATINO                0                 35
[1] 2 2
[1] FALSE

Clustering(48) Variable = 18P LOSS MUTATION ANALYSIS
D48V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    4  1
  18P LOSS WILD-TYPE 33  8
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                 41 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 1                  8 
$`18P LOSS MUTATED`
TCGA-FA-A4XK TCGA-FF-A7CX TCGA-G8-6325 TCGA-GS-A9TQ TCGA-RQ-AAAT 
       23.28        12.66        51.98        27.32         0.56 

$`18P LOSS WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         1.91        13.15        13.48         8.15 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       14.04        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FM-8000 
       27.35        22.32         9.80        10.29        26.01        31.96 
TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       41.16        47.38       211.23        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        36.13        42.71        43.86        57.17 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       112.24        18.25        47.84        37.22       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
       21.70        89.33        12.85        25.91         0.03 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.56               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             51.98             211.23 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             23.28              31.10 
[1] "0.6 - 52.0 (23.3)"  "0.0 - 211.2 (31.1)"
[1] "hr=" "1.6"
D48V2, continuous
D48V3, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    2  3
  18P LOSS WILD-TYPE 24 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    3
  18P LOSS WILD-TYPE   24   18
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                2                 24
  MALE                  3                 18
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  18P LOSS MUTATED                                                                                   4
  18P LOSS WILD-TYPE                                                                                36
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  18P LOSS MUTATED                          1
  18P LOSS WILD-TYPE                        2
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  18P LOSS MUTATED                                    0
  18P LOSS WILD-TYPE                                  4
D48V4, multiclass
                                                                                   clus
vv                                                                                  18P LOSS 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                                                                                  18P LOSS WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 36
  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
  18P LOSS MUTATED       2                         0     3
  18P LOSS WILD-TYPE    16                         1    25
D48V5, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    2                 16
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                 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"
D48V6, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    2  3
  18P LOSS WILD-TYPE 10 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    3
  18P LOSS WILD-TYPE   10   32
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                3                 32
[1] 2 2
[1] FALSE

Clustering(49) Variable = 18Q LOSS MUTATION ANALYSIS
D49V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    4  0
  18Q LOSS WILD-TYPE 33  9
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 42 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 0                  9 
$`18Q LOSS MUTATED`
TCGA-G8-6325 TCGA-GS-A9TQ TCGA-GS-A9TY TCGA-RQ-AAAT 
       51.98        27.32       109.58         0.56 

$`18Q LOSS 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        13.15        13.48 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
        8.15        14.04        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       12.66        31.96        41.16        47.38       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        36.13        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       43.86        57.17        38.24       112.24        18.25        47.84 
TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
       37.22        21.70        89.33        12.85        25.91         0.03 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.56               0.03 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            109.58             211.23 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             39.65              26.68 
[1] "0.6 - 109.6 (39.6)" "0.0 - 211.2 (26.7)"
[1] "hr="     "7.7e+07"
D49V2, continuous
D49V3, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    3  1
  18Q LOSS WILD-TYPE 23 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3    1
  18Q LOSS WILD-TYPE   23   20
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                3                 23
  MALE                  1                 20
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  18Q LOSS MUTATED                                                                                   3
  18Q LOSS WILD-TYPE                                                                                37
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  18Q LOSS MUTATED                          1
  18Q LOSS WILD-TYPE                        2
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  18Q LOSS MUTATED                                    0
  18Q LOSS WILD-TYPE                                  4
D49V4, multiclass
                                                                                   clus
vv                                                                                  18Q LOSS 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                                                                                  18Q LOSS 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
  18Q LOSS MUTATED       0                         0     4
  18Q LOSS WILD-TYPE    18                         1    24
D49V5, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    0                 18
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    4                 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"
D49V6, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    3  1
  18Q LOSS WILD-TYPE  9 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3    1
  18Q LOSS WILD-TYPE    9   34
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  9
  NOT HISPANIC OR LATINO                1                 34
[1] 2 2
[1] FALSE

Clustering(50) Variable = 22Q LOSS MUTATION ANALYSIS
D50V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED    3  0
  22Q LOSS WILD-TYPE 34  9
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                 43 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 0                  9 
$`22Q LOSS MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8043 
       13.15        14.04        31.73 

$`22Q LOSS 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        13.48         8.15 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.10        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66        31.96        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        47.38       211.23        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        36.13        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       27.32        38.24       112.24        18.25        47.84        37.22 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        21.70        89.33        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             13.15               0.03 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             31.73             211.23 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             14.04              27.35 
[1] "13.2 - 31.7 (14.0)" "0.0 - 211.2 (27.4)"
[1] "hr="     "7.4e+07"
D50V2, continuous
D50V3, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    3  0
  22Q LOSS WILD-TYPE 23 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3    0
  22Q LOSS WILD-TYPE   23   21
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                3                 23
  MALE                  0                 21
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  22Q LOSS MUTATED                                                                                   3
  22Q LOSS WILD-TYPE                                                                                37
                    vv
clus                 PRIMARY DLBCL OF THE CNS
  22Q LOSS MUTATED                          0
  22Q LOSS WILD-TYPE                        3
                    vv
clus                 PRIMARY MEDIASTINAL (THYMIC) DLBCL
  22Q LOSS MUTATED                                    0
  22Q LOSS WILD-TYPE                                  4
D50V4, multiclass
                                                                                   clus
vv                                                                                  22Q LOSS 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                                                                                  22Q LOSS 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
  22Q LOSS MUTATED       3                         0     0
  22Q LOSS WILD-TYPE    15                         1    28
D50V5, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    0                 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"
D50V6, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    0  3
  22Q LOSS WILD-TYPE 12 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      0    3
  22Q LOSS WILD-TYPE   12   32
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                3                 32
[1] 2 2
[1] FALSE

Clustering(51) Variable = XP LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  XP LOSS MUTATED    3  2
  XP LOSS WILD-TYPE 34  7
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                5                41 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                2                 7 
$`XP LOSS MUTATED`
TCGA-FA-A7Q1 TCGA-FF-8043 TCGA-FF-8047 TCGA-G8-6907 TCGA-GS-A9U3 
        8.15        31.73         4.14        19.56        89.33 

$`XP LOSS 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        13.15        13.48 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 
       14.04        35.54        31.10        24.69        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66        31.96        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       51.98        47.38       211.23       116.81       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       98.07        36.13        42.71        43.86        57.17        27.32 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       112.24        18.25        47.84        37.22       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       21.70        12.85        25.91         0.03         0.56 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             4.14              0.03 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            89.33            211.23 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            19.56             27.35 
[1] "4.1 - 89.3 (19.6)"  "0.0 - 211.2 (27.4)"
[1] "hr=" "4.2"
D51V2, continuous
D51V3, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    5  0
  XP LOSS WILD-TYPE 21 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      5    0
  XP LOSS WILD-TYPE   21   21
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE               5                21
  MALE                 0                21
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  XP LOSS MUTATED                                                                                   5
  XP LOSS WILD-TYPE                                                                                35
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  XP LOSS MUTATED                          0                                  0
  XP LOSS WILD-TYPE                        3                                  4
D51V4, multiclass
                                                                                   clus
vv                                                                                  XP LOSS 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                                                                                  XP LOSS 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
  XP LOSS MUTATED       3                         0     2
  XP LOSS WILD-TYPE    15                         1    26
D51V5, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   2                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"
D51V6, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    1  4
  XP LOSS WILD-TYPE 11 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      1    4
  XP LOSS WILD-TYPE   11   31
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               4                31
[1] 2 2
[1] FALSE

Clustering(52) Variable = XQ LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED    2  2
  XQ LOSS WILD-TYPE 35  7
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                42 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                 7 
$`XQ LOSS MUTATED`
TCGA-FA-A7Q1 TCGA-FF-8043 TCGA-FF-8047 TCGA-G8-6907 
        8.15        31.73         4.14        19.56 

$`XQ LOSS 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        13.15        13.48 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 
       14.04        35.54        31.10        24.69        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66        31.96        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       51.98        47.38       211.23       116.81       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       98.07        36.13        42.71        43.86        57.17        27.32 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       112.24        18.25        47.84        37.22       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       21.70        89.33        12.85        25.91         0.03         0.56 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             4.14              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            31.73            211.23 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           13.855            29.225 
[1] "4.1 - 31.7 (13.9)"  "0.0 - 211.2 (29.2)"
[1] "hr=" "7.7"
D52V2, continuous
D52V3, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    4  0
  XQ LOSS WILD-TYPE 22 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4    0
  XQ LOSS WILD-TYPE   22   21
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               4                22
  MALE                 0                21
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  XQ LOSS MUTATED                                                                                   4
  XQ LOSS WILD-TYPE                                                                                36
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  XQ LOSS MUTATED                          0                                  0
  XQ LOSS WILD-TYPE                        3                                  4
D52V4, multiclass
                                                                                   clus
vv                                                                                  XQ LOSS 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                                                                                  XQ LOSS 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
  XQ LOSS MUTATED       3                         0     1
  XQ LOSS WILD-TYPE    15                         1    27
D52V5, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   1                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"
D52V6, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    0  4
  XQ LOSS WILD-TYPE 12 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0    4
  XQ LOSS WILD-TYPE   12   31
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               4                31
[1] 2 2
[1] FALSE
