[1] "ofn"        "-oTDLBC-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/DLBC-TP/22506396/DLBC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/22516374/transformed.cor.cli.txt"

nPatients in clinical file=48, in cluster file=48, common to both=48
[1] "Reduce the number of clustering variables from 82 to 52."
[1] 52 48
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                6                42 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                6                42 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                42 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                42 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                42 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                42 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10                38 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10                38 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               13                35 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               13                35 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                41 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                41 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6                42 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6                42 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6                42 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6                42 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4                44 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4                44 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               14                34 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               14                34 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               12                36 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               12                36 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7                41 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7                41 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                8                40 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                8                40 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                7                41 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                7                41 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7                41 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7                41 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 44 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 44 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                 44 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                 44 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                 39 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                 39 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                13                 35 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                13                 35 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 7                 41 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 7                 41 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 9                 39 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 9                 39 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                 43 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                 43 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                 41 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                 41 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                 41 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                 41 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                 45 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                 45 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                13                 35 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                13                 35 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                13                 35 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                13                 35 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                 45 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                 45 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                 45 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                 45 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 5                 43 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 5                 43 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 4                 44 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 4                 44 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                 38 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                 38 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                6                42 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                6                42 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                7                41 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                7                41 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                45 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                45 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                4                44 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                4                44 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                45 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                45 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                3                45 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                3                45 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4                44 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4                44 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7                41 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7                41 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                8                40 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                8                40 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                44 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                44 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 3                 45 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 3                 45 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                 41 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                 41 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 44 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 44 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 9                 39 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 9                 39 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                 44 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                 44 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                 43 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                 43 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 5                 43 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 5                 43 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                 45 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                 45 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                5                43 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                5                43 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                44 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                44 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "NUMBER_OF_LYMPH_NODES"               
[15] "RACE"                                
[16] "ETHNICITY"                           

Input Data has 16 rows and 48 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=37,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NUMBER_OF_LYMPH_NODES is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 48 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"    "TUMOR_TISSUE_SITE" "GENDER"           
[4] "RADIATION_THERAPY" "HISTOLOGICAL_TYPE" "RACE"             
[7] "ETHNICITY"        
YEARS_TO_BIRTH, nv=34, binary=FALSE, numeric=TRUE
TUMOR_TISSUE_SITE, nv=13, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1Q GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED    5  0
  1Q GAIN WILD-TYPE 33  9
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                5                42 
  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        32.28 

$`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        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       24.69         4.14        27.35        22.32         9.80        10.29 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       26.01        12.66        41.16        70.06       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        51.98        42.71        43.86 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15       111.58        12.85        25.91         0.03         0.56 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            31.96              0.03 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            98.07            211.23 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            51.98             25.53 
[1] "32.0 - 98.1 (52.0)" "0.0 - 211.2 (25.5)"
[1] "hr="     "8.4e+07"
D1V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  1Q GAIN MUTATED         0                  0    0     0      0     1     0
  1Q GAIN WILD-TYPE       2                  2    4     3      1     1     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  1Q GAIN MUTATED                       0             0               0
  1Q GAIN WILD-TYPE                     1             1               3
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  1Q GAIN MUTATED                                               1       1
  1Q GAIN WILD-TYPE                                             0       1
                   vv
clus                THYROID
  1Q GAIN MUTATED         0
  1Q GAIN WILD-TYPE       2
D1V3, multiclass
                                               clus
vv                                              1Q GAIN MUTATED
  ADRENAL                                                     0
  ASCITES/PERITONEUM                                          0
  BONE                                                        0
  BRAIN                                                       0
  BREAST                                                      0
  COLON                                                       1
  LIVER                                                       0
  OTHER EXTRANODAL SITE                                       0
  PAROTID GLAND                                               0
  SMALL INTESTINE                                             0
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)               1
  STOMACH                                                     1
  THYROID                                                     0
                                               clus
vv                                              1Q GAIN WILD-TYPE
  ADRENAL                                                       2
  ASCITES/PERITONEUM                                            2
  BONE                                                          4
  BRAIN                                                         3
  BREAST                                                        1
  COLON                                                         1
  LIVER                                                         1
  OTHER EXTRANODAL SITE                                         1
  PAROTID GLAND                                                 1
  SMALL INTESTINE                                               3
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                 0
  STOMACH                                                       1
  THYROID                                                       2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    3  3
  1Q GAIN WILD-TYPE 23 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3    3
  1Q GAIN WILD-TYPE   23   19
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               3                23
  MALE                 3                19
[1] 2 2
[1] FALSE
D1V5, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    6  0
  1Q GAIN WILD-TYPE 34  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      6    0
  1Q GAIN WILD-TYPE   34    7
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                6                34
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  1Q GAIN MUTATED                                                                                   6
  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
D1V6, multiclass
                                                                                   clus
vv                                                                                  1Q GAIN MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               6
  PRIMARY DLBCL OF THE CNS                                                                        0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              0
                                                                                   clus
vv                                                                                  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     6
  1Q GAIN WILD-TYPE    18                         1    23
D1V7, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   0                18
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   6                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"
D1V8, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    1  5
  1Q GAIN WILD-TYPE 11 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1    5
  1Q GAIN WILD-TYPE   11   31
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               5                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 33  8
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                41 
  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        45.14       109.58        25.15 

$`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        24.62        23.64         8.15 
TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       18.18        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        70.06       211.23        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        98.07        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       57.17        32.28        38.24       128.12        24.00        53.16 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
      111.58        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 
           30.345            27.350 
[1] "14.0 - 109.6 (30.3)" "0.0 - 211.2 (27.4)" 
[1] "hr=" "1"  
D2V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  2P GAIN MUTATED         0                  0    0     0      0     0     0
  2P GAIN WILD-TYPE       2                  2    4     3      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  2P GAIN MUTATED                       0             0               2
  2P GAIN WILD-TYPE                     1             1               1
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  2P GAIN MUTATED                                               0       0
  2P GAIN WILD-TYPE                                             1       2
                   vv
clus                THYROID
  2P GAIN MUTATED         0
  2P GAIN WILD-TYPE       2
D2V3, multiclass
[1] "Remove cluster labels:" "2P GAIN MUTATED"       
clus
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                2                23 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A7DS        TCGA-FF-8043 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FF-A7CQ        TCGA-FF-A7CR 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FF-A7CW        TCGA-FF-A7CX        TCGA-FM-8000        TCGA-G8-6324 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G8-6326        TCGA-G8-6906        TCGA-GR-7351        TCGA-GR-A4D4 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GR-A4D5        TCGA-GR-A4D9        TCGA-GS-A9TT        TCGA-RQ-A68N 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-RQ-A6JB        TCGA-RQ-AAAT        TCGA-VB-A8QN 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
D2V4, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    3  3
  2P GAIN WILD-TYPE 23 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3    3
  2P GAIN WILD-TYPE   23   19
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               3                23
  MALE                 3                19
[1] 2 2
[1] FALSE
D2V5, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    4  2
  2P GAIN WILD-TYPE 36  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      4    2
  2P GAIN WILD-TYPE   36    5
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                4                36
  YES               2                 5
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  2P GAIN MUTATED                                                                                   4
  2P GAIN WILD-TYPE                                                                                37
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  2P GAIN MUTATED                          0                                  2
  2P GAIN WILD-TYPE                        3                                  2
D2V6, 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)                37
  PRIMARY DLBCL OF THE CNS                                                                          3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       3                         0     3
  2P GAIN WILD-TYPE    15                         1    26
D2V7, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    3  3
  2P GAIN WILD-TYPE  9 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3    3
  2P GAIN WILD-TYPE    9   33
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO               3                33
[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 33  8
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                41 
  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        45.14       109.58        25.15 

$`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        24.62        23.64         8.15 
TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       18.18        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        70.06       211.23        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        98.07        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       57.17        32.28        38.24       128.12        24.00        53.16 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
      111.58        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 
           30.345            27.350 
[1] "14.0 - 109.6 (30.3)" "0.0 - 211.2 (27.4)" 
[1] "hr=" "1"  
D3V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  2Q GAIN MUTATED         0                  0    0     0      0     0     0
  2Q GAIN WILD-TYPE       2                  2    4     3      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  2Q GAIN MUTATED                       0             0               2
  2Q GAIN WILD-TYPE                     1             1               1
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  2Q GAIN MUTATED                                               0       0
  2Q GAIN WILD-TYPE                                             1       2
                   vv
clus                THYROID
  2Q GAIN MUTATED         0
  2Q GAIN WILD-TYPE       2
D3V3, multiclass
[1] "Remove cluster labels:" "2Q GAIN MUTATED"       
clus
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                2                23 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A7DS        TCGA-FF-8043 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FF-8061        TCGA-FF-8062        TCGA-FF-A7CQ        TCGA-FF-A7CR 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FF-A7CW        TCGA-FF-A7CX        TCGA-FM-8000        TCGA-G8-6324 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G8-6326        TCGA-G8-6906        TCGA-GR-7351        TCGA-GR-A4D4 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GR-A4D5        TCGA-GR-A4D9        TCGA-GS-A9TT        TCGA-RQ-A68N 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-RQ-A6JB        TCGA-RQ-AAAT        TCGA-VB-A8QN 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
D3V4, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    3  3
  2Q GAIN WILD-TYPE 23 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3    3
  2Q GAIN WILD-TYPE   23   19
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               3                23
  MALE                 3                19
[1] 2 2
[1] FALSE
D3V5, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    4  2
  2Q GAIN WILD-TYPE 36  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4    2
  2Q GAIN WILD-TYPE   36    5
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                4                36
  YES               2                 5
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  2Q GAIN MUTATED                                                                                   4
  2Q GAIN WILD-TYPE                                                                                37
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  2Q GAIN MUTATED                          0                                  2
  2Q GAIN WILD-TYPE                        3                                  2
D3V6, 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)                37
  PRIMARY DLBCL OF THE CNS                                                                          3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       3                         0     3
  2Q GAIN WILD-TYPE    15                         1    26
D3V7, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    3  3
  2Q GAIN WILD-TYPE  9 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3    3
  2Q GAIN WILD-TYPE    9   33
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO               3                33
[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 28  9
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10                37 
  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 
       24.62        14.04        31.10        26.01       196.60        43.86 
TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9U3 TCGA-RQ-A68N 
       53.16        45.14       111.58        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        23.64         8.15 
TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       18.18        35.54        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-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-GR-7351 
       51.98        70.06       211.23        19.56       116.81       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT 
       98.07        51.98        42.71        57.17        32.28        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U4 TCGA-RQ-A6JB 
      128.12        24.00       109.58        25.15        12.85         0.03 
TCGA-RQ-AAAT 
        0.56 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            14.04              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           196.60            211.23 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            37.48             25.15 
[1] "14.0 - 196.6 (37.5)" "0.0 - 211.2 (25.1)" 
[1] "hr="     "2.9e+08"
D4V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  3P GAIN MUTATED         0                  0    0     1      0     0     0
  3P GAIN WILD-TYPE       2                  2    4     2      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  3P GAIN MUTATED                       0             1               1
  3P GAIN WILD-TYPE                     1             0               2
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  3P GAIN MUTATED                                               0       0
  3P GAIN WILD-TYPE                                             1       2
                   vv
clus                THYROID
  3P GAIN MUTATED         0
  3P GAIN WILD-TYPE       2
D4V3, multiclass
                                               clus
vv                                              3P GAIN MUTATED
  ADRENAL                                                     0
  ASCITES/PERITONEUM                                          0
  BONE                                                        0
  BRAIN                                                       1
  BREAST                                                      0
  COLON                                                       0
  LIVER                                                       0
  OTHER EXTRANODAL SITE                                       0
  PAROTID GLAND                                               1
  SMALL INTESTINE                                             1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)               0
  STOMACH                                                     0
  THYROID                                                     0
                                               clus
vv                                              3P GAIN WILD-TYPE
  ADRENAL                                                       2
  ASCITES/PERITONEUM                                            2
  BONE                                                          4
  BRAIN                                                         2
  BREAST                                                        1
  COLON                                                         2
  LIVER                                                         1
  OTHER EXTRANODAL SITE                                         1
  PAROTID GLAND                                                 0
  SMALL INTESTINE                                               2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                 1
  STOMACH                                                       2
  THYROID                                                       2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    6  4
  3P GAIN WILD-TYPE 20 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      6    4
  3P GAIN WILD-TYPE   20   18
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               6                20
  MALE                 4                18
[1] 2 2
[1] FALSE
D4V5, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    8  2
  3P GAIN WILD-TYPE 32  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      8    2
  3P GAIN WILD-TYPE   32    5
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                8                32
  YES               2                 5
[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                                                                                33
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  3P GAIN MUTATED                          1                                  1
  3P GAIN WILD-TYPE                        2                                  3
D4V6, 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)                33
  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    24
D4V7, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   5                13
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   5                24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    4  6
  3P GAIN WILD-TYPE  8 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4    6
  3P GAIN WILD-TYPE    8   30
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 8
  NOT HISPANIC OR LATINO               6                30
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3Q GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED   13  0
  3Q GAIN WILD-TYPE 25  9
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               13                34 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                0                 9 
$`3Q GAIN MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8047 TCGA-FF-A7CW 
       24.62        14.04        18.18        31.10         4.14        26.01 
TCGA-G8-6914 TCGA-GR-A4D6 TCGA-GS-A9TU TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9U3 
      196.60        43.86       128.12        53.16        45.14       111.58 
TCGA-RQ-A68N 
       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        23.64         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        70.06 
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        51.98 
TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TV TCGA-GS-A9TY 
       42.71        57.17        32.28        38.24        24.00       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U4 TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15        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 
            31.10             26.25 
[1] "4.1 - 196.6 (31.1)" "0.0 - 211.2 (26.2)"
[1] "hr="     "3.4e+08"
D5V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  3Q GAIN MUTATED         0                  0    0     1      0     0     0
  3Q GAIN WILD-TYPE       2                  2    4     2      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  3Q GAIN MUTATED                       0             1               1
  3Q GAIN WILD-TYPE                     1             0               2
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  3Q GAIN MUTATED                                               0       0
  3Q GAIN WILD-TYPE                                             1       2
                   vv
clus                THYROID
  3Q GAIN MUTATED         0
  3Q GAIN WILD-TYPE       2
D5V3, multiclass
                                               clus
vv                                              3Q GAIN MUTATED
  ADRENAL                                                     0
  ASCITES/PERITONEUM                                          0
  BONE                                                        0
  BRAIN                                                       1
  BREAST                                                      0
  COLON                                                       0
  LIVER                                                       0
  OTHER EXTRANODAL SITE                                       0
  PAROTID GLAND                                               1
  SMALL INTESTINE                                             1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)               0
  STOMACH                                                     0
  THYROID                                                     0
                                               clus
vv                                              3Q GAIN WILD-TYPE
  ADRENAL                                                       2
  ASCITES/PERITONEUM                                            2
  BONE                                                          4
  BRAIN                                                         2
  BREAST                                                        1
  COLON                                                         2
  LIVER                                                         1
  OTHER EXTRANODAL SITE                                         1
  PAROTID GLAND                                                 0
  SMALL INTESTINE                                               2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                 1
  STOMACH                                                       2
  THYROID                                                       2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    8  5
  3Q GAIN WILD-TYPE 18 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      8    5
  3Q GAIN WILD-TYPE   18   17
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               8                18
  MALE                 5                17
[1] 2 2
[1] FALSE
D5V5, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   10  3
  3Q GAIN WILD-TYPE 30  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     10    3
  3Q GAIN WILD-TYPE   30    4
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               10                30
  YES               3                 4
[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                                                                                30
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  3Q GAIN MUTATED                          1                                  1
  3Q GAIN WILD-TYPE                        2                                  3
D5V6, 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)                30
  PRIMARY DLBCL OF THE CNS                                                                          2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       6                         0     7
  3Q GAIN WILD-TYPE    12                         1    22
D5V7, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   6                12
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   7                22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    5  8
  3Q GAIN WILD-TYPE  7 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5    8
  3Q GAIN WILD-TYPE    7   28
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 7
  NOT HISPANIC OR LATINO               8                28
[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 33  7
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                40 
  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        53.16        45.14       109.58 
TCGA-GS-A9TZ 
       25.15 

$`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        24.62        23.64 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       14.04        18.18        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       31.96        41.16        51.98        70.06       211.23        19.56 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        98.07        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9U3 
       57.17        32.28        38.24       128.12        24.00       111.58 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85        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 
            45.14             25.96 
[1] "8.2 - 116.8 (45.1)" "0.0 - 211.2 (26.0)"
[1] "hr=" "1.5"
D6V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  5P GAIN MUTATED         0                  0    0     0      0     0     0
  5P GAIN WILD-TYPE       2                  2    4     3      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  5P GAIN MUTATED                       0             0               0
  5P GAIN WILD-TYPE                     1             1               3
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  5P GAIN MUTATED                                               0       0
  5P GAIN WILD-TYPE                                             1       2
                   vv
clus                THYROID
  5P GAIN MUTATED         0
  5P GAIN WILD-TYPE       2
D6V3, multiclass
D6V4, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    4  3
  5P GAIN WILD-TYPE 22 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      4    3
  5P GAIN WILD-TYPE   22   19
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               4                22
  MALE                 3                19
[1] 2 2
[1] FALSE
D6V5, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    4  3
  5P GAIN WILD-TYPE 36  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      4    3
  5P GAIN WILD-TYPE   36    4
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                4                36
  YES               3                 4
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  5P GAIN MUTATED                                                                                   4
  5P GAIN WILD-TYPE                                                                                37
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  5P GAIN MUTATED                          0                                  3
  5P GAIN WILD-TYPE                        3                                  1
D6V6, 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)                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
  5P GAIN MUTATED       2                         0     5
  5P GAIN WILD-TYPE    16                         1    24
D6V7, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   2                16
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   5                24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    4  3
  5P GAIN WILD-TYPE  8 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      4    3
  5P GAIN WILD-TYPE    8   33
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 8
  NOT HISPANIC OR LATINO               3                33
[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 33  8
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                6                41 
  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        53.16        45.14       109.58        25.15 

$`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        24.62        23.64 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       14.04        18.18        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       31.96        41.16        51.98        70.06       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
      116.81       196.60       150.51        98.07        51.98        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV 
       43.86        57.17        32.28        38.24       128.12        24.00 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
      111.58        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 
            40.34             26.01 
[1] "8.2 - 109.6 (40.3)" "0.0 - 211.2 (26.0)"
[1] "hr=" "1"  
D7V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  5Q GAIN MUTATED         0                  0    0     0      0     0     0
  5Q GAIN WILD-TYPE       2                  2    4     3      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  5Q GAIN MUTATED                       0             0               0
  5Q GAIN WILD-TYPE                     1             1               3
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  5Q GAIN MUTATED                                               0       0
  5Q GAIN WILD-TYPE                                             1       2
                   vv
clus                THYROID
  5Q GAIN MUTATED         0
  5Q GAIN WILD-TYPE       2
D7V3, multiclass
D7V4, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    4  2
  5Q GAIN WILD-TYPE 22 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      4    2
  5Q GAIN WILD-TYPE   22   20
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               4                22
  MALE                 2                20
[1] 2 2
[1] FALSE
D7V5, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    3  3
  5Q GAIN WILD-TYPE 37  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3    3
  5Q GAIN WILD-TYPE   37    4
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                3                37
  YES               3                 4
[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                                                                                38
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  5Q GAIN MUTATED                          0                                  3
  5Q GAIN WILD-TYPE                        3                                  1
D7V6, 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)                38
  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    25
D7V7, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   2                16
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   4                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    4  2
  5Q GAIN WILD-TYPE  8 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      4    2
  5Q GAIN WILD-TYPE    8   34
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 8
  NOT HISPANIC OR LATINO               2                34
[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 32  9
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6                41 
  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 
       24.62        14.04        31.10        51.98        32.28        53.16 

$`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        23.64         8.15 
TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       18.18        35.54        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       41.16        70.06       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        51.98        42.71        43.86        57.17 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
       38.24       128.12        24.00        45.14       109.58        25.15 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
      111.58        12.85        25.91         0.03         0.56 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            14.04              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            53.16            211.23 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            31.69             26.01 
[1] "14.0 - 53.2 (31.7)" "0.0 - 211.2 (26.0)"
[1] "hr="     "8.5e+07"
D8V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  6P GAIN MUTATED         0                  0    0     0      0     0     0
  6P GAIN WILD-TYPE       2                  2    4     3      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  6P GAIN MUTATED                       0             0               1
  6P GAIN WILD-TYPE                     1             1               2
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  6P GAIN MUTATED                                               0       0
  6P GAIN WILD-TYPE                                             1       2
                   vv
clus                THYROID
  6P GAIN MUTATED         0
  6P GAIN WILD-TYPE       2
D8V3, multiclass
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                24 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A7DS 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FF-8043        TCGA-FF-8061        TCGA-FF-8062        TCGA-FF-A7CQ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FF-A7CR        TCGA-FF-A7CW        TCGA-FF-A7CX        TCGA-FM-8000 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6326        TCGA-G8-6906        TCGA-GR-7351 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D9        TCGA-GS-A9TT 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-RQ-AAAT        TCGA-VB-A8QN 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D8V4, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    5  1
  6P GAIN WILD-TYPE 21 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5    1
  6P GAIN WILD-TYPE   21   21
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               5                21
  MALE                 1                21
[1] 2 2
[1] FALSE
D8V5, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    5  1
  6P GAIN WILD-TYPE 35  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5    1
  6P GAIN WILD-TYPE   35    6
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                5                35
  YES               1                 6
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  6P GAIN MUTATED                                                                                   5
  6P GAIN WILD-TYPE                                                                                36
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  6P GAIN MUTATED                          0                                  1
  6P GAIN WILD-TYPE                        3                                  3
D8V6, 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)                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
  6P GAIN MUTATED       3                         0     3
  6P GAIN WILD-TYPE    15                         1    26
D8V7, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    2  4
  6P GAIN WILD-TYPE 10 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2    4
  6P GAIN WILD-TYPE   10   32
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO               4                32
[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 34  9
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4                43 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                0                 9 
$`6Q GAIN MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8042 TCGA-GS-A9TQ 
       24.62        14.04        31.10        32.28 

$`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        23.64         8.15 
TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       18.18        35.54        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        70.06       211.23        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        98.07        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       57.17        38.24       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            14.04              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            32.28            211.23 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            27.86             27.35 
[1] "14.0 - 32.3 (27.9)" "0.0 - 211.2 (27.4)"
[1] "hr="     "7.7e+07"
D9V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  6Q GAIN MUTATED         0                  0    0     0      0     0     0
  6Q GAIN WILD-TYPE       2                  2    4     3      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  6Q GAIN MUTATED                       0             0               1
  6Q GAIN WILD-TYPE                     1             1               2
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  6Q GAIN MUTATED                                               0       0
  6Q GAIN WILD-TYPE                                             1       2
                   vv
clus                THYROID
  6Q GAIN MUTATED         0
  6Q GAIN WILD-TYPE       2
D9V3, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1                24 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A7DS 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FF-8043        TCGA-FF-8061        TCGA-FF-8062        TCGA-FF-A7CQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FF-A7CR        TCGA-FF-A7CW        TCGA-FF-A7CX        TCGA-FM-8000 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6326        TCGA-G8-6906        TCGA-GR-7351 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D9        TCGA-GS-A9TT 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-RQ-AAAT        TCGA-VB-A8QN 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D9V4, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    4  0
  6Q GAIN WILD-TYPE 22 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      4    0
  6Q GAIN WILD-TYPE   22   22
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               4                22
  MALE                 0                22
[1] 2 2
[1] FALSE
D9V5, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    4  0
  6Q GAIN WILD-TYPE 36  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      4    0
  6Q GAIN WILD-TYPE   36    7
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                4                36
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  6Q GAIN MUTATED                                                                                   4
  6Q GAIN WILD-TYPE                                                                                37
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  6Q GAIN MUTATED                          0                                  0
  6Q GAIN WILD-TYPE                        3                                  4
D9V6, 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)                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
  6Q GAIN MUTATED       3                         0     1
  6Q GAIN WILD-TYPE    15                         1    28
D9V7, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   1                28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    1  3
  6Q GAIN WILD-TYPE 11 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    3
  6Q GAIN WILD-TYPE   11   33
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               3                33
[1] 2 2
[1] FALSE

Clustering(10) Variable = 7P GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   13  1
  7P GAIN WILD-TYPE 25  8
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               14                33 
  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        24.62        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        51.98        43.86        32.28       128.12 
TCGA-GS-A9TX TCGA-GS-A9U3 
       45.14       111.58 

$`7P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A86F 
        4.34         4.34         1.91        23.64         8.15        18.18 
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-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
        9.80        10.29        12.66        41.16        51.98        70.06 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-A4D5 TCGA-GR-A4D9 
      211.23        19.56       116.81       150.51        42.71        57.17 
TCGA-GS-A9TT TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U4 
       38.24        24.00        53.16       109.58        25.15        12.85 
TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.91         0.03         0.56 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            14.04              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           196.60            211.23 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            38.07             24.69 
[1] "14.0 - 196.6 (38.1)" "0.0 - 211.2 (24.7)" 
[1] "hr=" "4.2"
D10V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  7P GAIN MUTATED         0                  0    1     0      0     1     0
  7P GAIN WILD-TYPE       2                  2    3     3      1     1     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  7P GAIN MUTATED                       0             1               2
  7P GAIN WILD-TYPE                     1             0               1
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  7P GAIN MUTATED                                               0       0
  7P GAIN WILD-TYPE                                             1       2
                   vv
clus                THYROID
  7P GAIN MUTATED         0
  7P GAIN WILD-TYPE       2
D10V3, multiclass
                                               clus
vv                                              7P GAIN MUTATED
  ADRENAL                                                     0
  ASCITES/PERITONEUM                                          0
  BONE                                                        1
  BRAIN                                                       0
  BREAST                                                      0
  COLON                                                       1
  LIVER                                                       0
  OTHER EXTRANODAL SITE                                       0
  PAROTID GLAND                                               1
  SMALL INTESTINE                                             2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)               0
  STOMACH                                                     0
  THYROID                                                     0
                                               clus
vv                                              7P GAIN WILD-TYPE
  ADRENAL                                                       2
  ASCITES/PERITONEUM                                            2
  BONE                                                          3
  BRAIN                                                         3
  BREAST                                                        1
  COLON                                                         1
  LIVER                                                         1
  OTHER EXTRANODAL SITE                                         1
  PAROTID GLAND                                                 0
  SMALL INTESTINE                                               1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                 1
  STOMACH                                                       2
  THYROID                                                       2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    8  6
  7P GAIN WILD-TYPE 18 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      8    6
  7P GAIN WILD-TYPE   18   16
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               8                18
  MALE                 6                16
[1] 2 2
[1] FALSE
D10V5, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   12  2
  7P GAIN WILD-TYPE 28  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     12    2
  7P GAIN WILD-TYPE   28    5
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               12                28
  YES               2                 5
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  7P GAIN MUTATED                                                                                  14
  7P GAIN WILD-TYPE                                                                                27
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  7P GAIN MUTATED                          0                                  0
  7P GAIN WILD-TYPE                        3                                  4
D10V6, multiclass
                                                                                   clus
vv                                                                                  7P GAIN MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)              14
  PRIMARY DLBCL OF THE CNS                                                                        0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                              0
                                                                                   clus
vv                                                                                  7P 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
  7P GAIN MUTATED       6                         0     8
  7P GAIN WILD-TYPE    12                         1    21
D10V7, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   6                12
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   8                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"
D10V8, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    4 10
  7P GAIN WILD-TYPE  8 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4   10
  7P GAIN WILD-TYPE    8   26
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 8
  NOT HISPANIC OR LATINO              10                26
[1] 2 2
[1] FALSE

Clustering(11) Variable = 7Q GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   11  1
  7Q GAIN WILD-TYPE 27  8
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               12                35 
  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        24.62        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        51.98        43.86        32.28       128.12        45.14 

$`7Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A86F 
        4.34         4.34         1.91        23.64         8.15        18.18 
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-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
        9.80        10.29        12.66        41.16        51.98        70.06 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D5 
      211.23        19.56       116.81       196.60       150.51        42.71 
TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TY TCGA-GS-A9TZ 
       57.17        38.24        24.00        53.16       109.58        25.15 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
      111.58        12.85        25.91         0.03         0.56 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            14.04              0.03 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           128.12            211.23 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            32.12             25.15 
[1] "14.0 - 128.1 (32.1)" "0.0 - 211.2 (25.1)" 
[1] "hr=" "2.9"
D11V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  7Q GAIN MUTATED         0                  0    1     0      0     1     0
  7Q GAIN WILD-TYPE       2                  2    3     3      1     1     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  7Q GAIN MUTATED                       0             1               2
  7Q GAIN WILD-TYPE                     1             0               1
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  7Q GAIN MUTATED                                               0       0
  7Q GAIN WILD-TYPE                                             1       2
                   vv
clus                THYROID
  7Q GAIN MUTATED         0
  7Q GAIN WILD-TYPE       2
D11V3, multiclass
                                               clus
vv                                              7Q GAIN MUTATED
  ADRENAL                                                     0
  ASCITES/PERITONEUM                                          0
  BONE                                                        1
  BRAIN                                                       0
  BREAST                                                      0
  COLON                                                       1
  LIVER                                                       0
  OTHER EXTRANODAL SITE                                       0
  PAROTID GLAND                                               1
  SMALL INTESTINE                                             2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)               0
  STOMACH                                                     0
  THYROID                                                     0
                                               clus
vv                                              7Q GAIN WILD-TYPE
  ADRENAL                                                       2
  ASCITES/PERITONEUM                                            2
  BONE                                                          3
  BRAIN                                                         3
  BREAST                                                        1
  COLON                                                         1
  LIVER                                                         1
  OTHER EXTRANODAL SITE                                         1
  PAROTID GLAND                                                 0
  SMALL INTESTINE                                               1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                 1
  STOMACH                                                       2
  THYROID                                                       2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V4, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    7  5
  7Q GAIN WILD-TYPE 19 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7    5
  7Q GAIN WILD-TYPE   19   17
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               7                19
  MALE                 5                17
[1] 2 2
[1] FALSE
D11V5, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   10  2
  7Q GAIN WILD-TYPE 30  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     10    2
  7Q GAIN WILD-TYPE   30    5
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               10                30
  YES               2                 5
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  7Q GAIN MUTATED                                                                                  12
  7Q GAIN WILD-TYPE                                                                                29
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  7Q GAIN MUTATED                          0                                  0
  7Q GAIN WILD-TYPE                        3                                  4
D11V6, multiclass
                                                                                   clus
vv                                                                                  7Q 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                                                              0
                                                                                   clus
vv                                                                                  7Q GAIN WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                29
  PRIMARY DLBCL OF THE CNS                                                                          3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       6                         0     6
  7Q GAIN WILD-TYPE    12                         1    23
D11V7, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   6                12
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   6                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"
D11V8, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    3  9
  7Q GAIN WILD-TYPE  9 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3    9
  7Q GAIN WILD-TYPE    9   27
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO               9                27
[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 32  8
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                7                40 
  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        32.28        53.16        45.14       111.58 
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        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
        8.15        14.04        18.18        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       12.66        31.96        41.16        51.98        70.06       211.23 
TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GR-A4D5 
       19.56       116.81       196.60       150.51        51.98        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TY 
       43.86        57.17        38.24       128.12        24.00       109.58 
TCGA-GS-A9TZ TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15        25.91         0.03         0.56 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            12.85              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           111.58            211.23 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            45.14             25.53 
[1] "12.8 - 111.6 (45.1)" "0.0 - 211.2 (25.5)" 
[1] "hr=" "1.4"
D12V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  8P GAIN MUTATED         0                  0    0     0      0     0     0
  8P GAIN WILD-TYPE       2                  2    4     3      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  8P GAIN MUTATED                       0             0               0
  8P GAIN WILD-TYPE                     1             1               3
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  8P GAIN MUTATED                                               0       0
  8P GAIN WILD-TYPE                                             1       2
                   vv
clus                THYROID
  8P GAIN MUTATED         0
  8P GAIN WILD-TYPE       2
D12V3, multiclass
D12V4, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    5  2
  8P GAIN WILD-TYPE 21 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5    2
  8P GAIN WILD-TYPE   21   20
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               5                21
  MALE                 2                20
[1] 2 2
[1] FALSE
D12V5, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    5  2
  8P GAIN WILD-TYPE 35  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5    2
  8P GAIN WILD-TYPE   35    5
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                5                35
  YES               2                 5
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  8P GAIN MUTATED                                                                                   5
  8P GAIN WILD-TYPE                                                                                36
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  8P GAIN MUTATED                          0                                  2
  8P GAIN WILD-TYPE                        3                                  2
D12V6, 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)                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
  8P GAIN MUTATED       1                         0     6
  8P GAIN WILD-TYPE    17                         1    23
D12V7, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   1                17
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   6                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"
D12V8, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    5  2
  8P GAIN WILD-TYPE  7 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5    2
  8P GAIN WILD-TYPE    7   34
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 7
  NOT HISPANIC OR LATINO               2                34
[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 31  8
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                8                39 
  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        32.28        53.16        45.14        25.15 
TCGA-GS-A9U3 TCGA-GS-A9U4 
      111.58        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        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
        8.15        14.04        18.18        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       12.66        31.96        41.16        51.98        70.06       211.23 
TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GR-A4D5 
       19.56       116.81       196.60       150.51        51.98        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TY 
       43.86        57.17        38.24       128.12        24.00       109.58 
TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.91         0.03         0.56 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            12.85              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           111.58            211.23 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            40.34             25.91 
[1] "12.8 - 111.6 (40.3)" "0.0 - 211.2 (25.9)" 
[1] "hr=" "1.6"
D13V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  8Q GAIN MUTATED         0                  0    0     0      0     0     0
  8Q GAIN WILD-TYPE       2                  2    4     3      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  8Q GAIN MUTATED                       0             0               0
  8Q GAIN WILD-TYPE                     1             1               3
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  8Q GAIN MUTATED                                               0       0
  8Q GAIN WILD-TYPE                                             1       2
                   vv
clus                THYROID
  8Q GAIN MUTATED         0
  8Q GAIN WILD-TYPE       2
D13V3, multiclass
D13V4, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    5  3
  8Q GAIN WILD-TYPE 21 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5    3
  8Q GAIN WILD-TYPE   21   19
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               5                21
  MALE                 3                19
[1] 2 2
[1] FALSE
D13V5, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    5  3
  8Q GAIN WILD-TYPE 35  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5    3
  8Q GAIN WILD-TYPE   35    4
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                5                35
  YES               3                 4
[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                                                                                36
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  8Q GAIN MUTATED                          0                                  3
  8Q GAIN WILD-TYPE                        3                                  1
D13V6, 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)                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
  8Q GAIN MUTATED       1                         0     7
  8Q GAIN WILD-TYPE    17                         1    22
D13V7, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   1                17
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   7                22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    6  2
  8Q GAIN WILD-TYPE  6 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6    2
  8Q GAIN WILD-TYPE    6   34
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                 6
  NOT HISPANIC OR LATINO               2                34
[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 32  8
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                7                40 
  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        24.00        53.16 
TCGA-GS-A9TZ 
       25.15 

$`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        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       14.04        18.18        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
       27.35        22.32        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        70.06       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        51.98        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9U3 
       32.28        38.24       128.12        45.14       109.58       111.58 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85        25.91         0.03         0.56 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             9.80              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            53.16            211.23 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           25.150            31.415 
[1] "9.8 - 53.2 (25.1)"  "0.0 - 211.2 (31.4)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  9P GAIN MUTATED         1                  0    0     0      0     0     0
  9P GAIN WILD-TYPE       1                  2    4     3      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  9P GAIN MUTATED                       0             1               1
  9P GAIN WILD-TYPE                     1             0               2
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  9P GAIN MUTATED                                               0       0
  9P GAIN WILD-TYPE                                             1       2
                   vv
clus                THYROID
  9P GAIN MUTATED         0
  9P GAIN WILD-TYPE       2
D14V3, multiclass
                                               clus
vv                                              9P GAIN MUTATED
  ADRENAL                                                     1
  ASCITES/PERITONEUM                                          0
  BONE                                                        0
  BRAIN                                                       0
  BREAST                                                      0
  COLON                                                       0
  LIVER                                                       0
  OTHER EXTRANODAL SITE                                       0
  PAROTID GLAND                                               1
  SMALL INTESTINE                                             1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)               0
  STOMACH                                                     0
  THYROID                                                     0
                                               clus
vv                                              9P GAIN WILD-TYPE
  ADRENAL                                                       1
  ASCITES/PERITONEUM                                            2
  BONE                                                          4
  BRAIN                                                         3
  BREAST                                                        1
  COLON                                                         2
  LIVER                                                         1
  OTHER EXTRANODAL SITE                                         1
  PAROTID GLAND                                                 0
  SMALL INTESTINE                                               2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                 1
  STOMACH                                                       2
  THYROID                                                       2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V4, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    3  4
  9P GAIN WILD-TYPE 23 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    4
  9P GAIN WILD-TYPE   23   18
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               3                23
  MALE                 4                18
[1] 2 2
[1] FALSE
D14V5, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    4  3
  9P GAIN WILD-TYPE 36  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      4    3
  9P GAIN WILD-TYPE   36    4
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                4                36
  YES               3                 4
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  9P GAIN MUTATED                                                                                   3
  9P GAIN WILD-TYPE                                                                                38
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  9P GAIN MUTATED                          0                                  4
  9P GAIN WILD-TYPE                        3                                  0
D14V6, 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)                38
  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    26
D14V7, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   4                14
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    3  4
  9P GAIN WILD-TYPE  9 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    4
  9P GAIN WILD-TYPE    9   32
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO               4                32
[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 32  8
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7                40 
  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        53.16        45.14 
TCGA-GS-A9TZ 
       25.15 

$`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        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       14.04        18.18        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
       27.35        22.32        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        70.06       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        51.98        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TY TCGA-GS-A9U3 
       32.28        38.24       128.12        24.00       109.58       111.58 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85        25.91         0.03         0.56 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             9.80              0.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            53.16            211.23 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           26.010            29.225 
[1] "9.8 - 53.2 (26.0)"  "0.0 - 211.2 (29.2)"
[1] "hr=" "1.1"
D15V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  9Q GAIN MUTATED         1                  0    0     0      0     0     0
  9Q GAIN WILD-TYPE       1                  2    4     3      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  9Q GAIN MUTATED                       0             1               1
  9Q GAIN WILD-TYPE                     1             0               2
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  9Q GAIN MUTATED                                               0       0
  9Q GAIN WILD-TYPE                                             1       2
                   vv
clus                THYROID
  9Q GAIN MUTATED         0
  9Q GAIN WILD-TYPE       2
D15V3, multiclass
                                               clus
vv                                              9Q GAIN MUTATED
  ADRENAL                                                     1
  ASCITES/PERITONEUM                                          0
  BONE                                                        0
  BRAIN                                                       0
  BREAST                                                      0
  COLON                                                       0
  LIVER                                                       0
  OTHER EXTRANODAL SITE                                       0
  PAROTID GLAND                                               1
  SMALL INTESTINE                                             1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)               0
  STOMACH                                                     0
  THYROID                                                     0
                                               clus
vv                                              9Q GAIN WILD-TYPE
  ADRENAL                                                       1
  ASCITES/PERITONEUM                                            2
  BONE                                                          4
  BRAIN                                                         3
  BREAST                                                        1
  COLON                                                         2
  LIVER                                                         1
  OTHER EXTRANODAL SITE                                         1
  PAROTID GLAND                                                 0
  SMALL INTESTINE                                               2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                 1
  STOMACH                                                       2
  THYROID                                                       2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V4, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    2  5
  9Q GAIN WILD-TYPE 24 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2    5
  9Q GAIN WILD-TYPE   24   17
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               2                24
  MALE                 5                17
[1] 2 2
[1] FALSE
D15V5, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    4  3
  9Q GAIN WILD-TYPE 36  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4    3
  9Q GAIN WILD-TYPE   36    4
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                4                36
  YES               3                 4
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  9Q GAIN MUTATED                                                                                   4
  9Q GAIN WILD-TYPE                                                                                37
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  9Q GAIN MUTATED                          0                                  3
  9Q GAIN WILD-TYPE                        3                                  1
D15V6, 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)                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
  9Q GAIN MUTATED       4                         0     3
  9Q GAIN WILD-TYPE    14                         1    26
D15V7, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   4                14
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    3  4
  9Q GAIN WILD-TYPE  9 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3    4
  9Q GAIN WILD-TYPE    9   32
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO               4                32
[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 34  9
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 43 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 0                  9 
$`10P GAIN MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-GR-A4D4 TCGA-GS-A9TQ 
       24.62        14.04        51.98        32.28 

$`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        23.64         8.15 
TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       18.18        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       31.96        41.16        51.98        70.06       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 
      116.81       196.60       150.51        98.07        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       57.17        38.24       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             14.04               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             51.98             211.23 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             28.45              27.35 
[1] "14.0 - 52.0 (28.5)" "0.0 - 211.2 (27.4)"
[1] "hr="     "7.7e+07"
D16V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  10P GAIN MUTATED         0                  0    1     0      0     0     0
  10P GAIN WILD-TYPE       2                  2    3     3      1     2     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  10P GAIN MUTATED                       0             0               1
  10P GAIN WILD-TYPE                     1             1               2
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  10P GAIN MUTATED                                               0       0
  10P GAIN WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  10P GAIN MUTATED         0
  10P GAIN WILD-TYPE       2
D16V3, multiclass
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 23 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FA-A7DS         TCGA-FF-8043         TCGA-FF-8061 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FF-A7CQ         TCGA-FF-A7CR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FF-A7CW         TCGA-FF-A7CX         TCGA-FM-8000 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G8-6324         TCGA-G8-6326         TCGA-G8-6906 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-A4D5         TCGA-GR-A4D9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GS-A9TT         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-RQ-AAAT         TCGA-VB-A8QN 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
D16V4, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    4  0
  10P GAIN WILD-TYPE 22 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4    0
  10P GAIN WILD-TYPE   22   22
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                4                 22
  MALE                  0                 22
[1] 2 2
[1] FALSE
D16V5, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    4  0
  10P GAIN WILD-TYPE 36  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4    0
  10P GAIN WILD-TYPE   36    7
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 4                 36
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  10P GAIN MUTATED                                                                                   4
  10P GAIN WILD-TYPE                                                                                37
                    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
D16V6, 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)                 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
  10P GAIN MUTATED       2                         0     2
  10P GAIN WILD-TYPE    16                         1    27
D16V7, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    2                 16
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    1  3
  10P GAIN WILD-TYPE 11 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1    3
  10P GAIN WILD-TYPE   11   33
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO                3                 33
[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 34  9
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                 43 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 0                  9 
$`10Q GAIN MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-GS-A9TQ TCGA-GS-A9TT 
       24.62        14.04        32.28        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        23.64         8.15 
TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       18.18        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       31.96        41.16        51.98        70.06       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
      116.81       196.60       150.51        98.07        51.98        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       43.86        57.17       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             14.04               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             38.24             211.23 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             28.45              27.35 
[1] "14.0 - 38.2 (28.5)" "0.0 - 211.2 (27.4)"
[1] "hr="     "7.7e+07"
D17V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  10Q GAIN MUTATED         0                  0    1     0      0     0     0
  10Q GAIN WILD-TYPE       2                  2    3     3      1     2     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  10Q GAIN MUTATED                       0             0               1
  10Q GAIN WILD-TYPE                     1             1               2
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  10Q GAIN MUTATED                                               0       0
  10Q GAIN WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  10Q GAIN MUTATED         0
  10Q GAIN WILD-TYPE       2
D17V3, multiclass
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 23 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FA-A7DS         TCGA-FF-8043         TCGA-FF-8061 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FF-A7CQ         TCGA-FF-A7CR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FF-A7CW         TCGA-FF-A7CX         TCGA-FM-8000 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G8-6324         TCGA-G8-6326         TCGA-G8-6906 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-A4D4         TCGA-GR-A4D5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GR-A4D9         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-RQ-AAAT         TCGA-VB-A8QN 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D17V4, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    3  1
  10Q GAIN WILD-TYPE 23 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    1
  10Q GAIN WILD-TYPE   23   21
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                3                 23
  MALE                  1                 21
[1] 2 2
[1] FALSE
D17V5, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    3  1
  10Q GAIN WILD-TYPE 37  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    1
  10Q GAIN WILD-TYPE   37    6
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 3                 37
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  10Q GAIN MUTATED                                                                                   4
  10Q GAIN WILD-TYPE                                                                                37
                    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
D17V6, 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)                 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
  10Q GAIN MUTATED       2                         0     2
  10Q GAIN WILD-TYPE    16                         1    27
D17V7, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    2                 16
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    2  2
  10Q GAIN WILD-TYPE 10 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    2
  10Q GAIN WILD-TYPE   10   34
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                2                 34
[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 30  8
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                 38 
  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        32.28        53.16 
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        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 
        8.15        18.18        35.54        31.10        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       31.96        41.16        51.98        70.06       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
      116.81       196.60       150.51        98.07        51.98        43.86 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
       38.24       128.12        24.00        45.14       109.58        25.15 
TCGA-GS-A9U3 TCGA-RQ-A6JB 
      111.58         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 
             31.73              26.68 
[1] "0.6 - 57.2 (31.7)"  "0.0 - 211.2 (26.7)"
[1] "hr=" "1.4"
D18V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  11P GAIN MUTATED         0                  0    1     2      0     1     0
  11P GAIN WILD-TYPE       2                  2    3     1      1     1     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  11P GAIN MUTATED                       0             0               1
  11P GAIN WILD-TYPE                     1             1               2
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  11P GAIN MUTATED                                               1       0
  11P GAIN WILD-TYPE                                             0       2
                    vv
clus                 THYROID
  11P GAIN MUTATED         0
  11P GAIN WILD-TYPE       2
D18V3, multiclass
                                               clus
vv                                              11P GAIN MUTATED
  ADRENAL                                                      0
  ASCITES/PERITONEUM                                           0
  BONE                                                         1
  BRAIN                                                        2
  BREAST                                                       0
  COLON                                                        1
  LIVER                                                        0
  OTHER EXTRANODAL SITE                                        0
  PAROTID GLAND                                                0
  SMALL INTESTINE                                              1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                1
  STOMACH                                                      0
  THYROID                                                      0
                                               clus
vv                                              11P GAIN WILD-TYPE
  ADRENAL                                                        2
  ASCITES/PERITONEUM                                             2
  BONE                                                           3
  BRAIN                                                          1
  BREAST                                                         1
  COLON                                                          1
  LIVER                                                          1
  OTHER EXTRANODAL SITE                                          1
  PAROTID GLAND                                                  1
  SMALL INTESTINE                                                2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                  0
  STOMACH                                                        2
  THYROID                                                        2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V4, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    8  1
  11P GAIN WILD-TYPE 18 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      8    1
  11P GAIN WILD-TYPE   18   21
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                8                 18
  MALE                  1                 21
[1] 2 2
[1] FALSE
D18V5, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    8  1
  11P GAIN WILD-TYPE 32  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      8    1
  11P GAIN WILD-TYPE   32    6
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 8                 32
  YES                1                  6
[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                                                                                35
                    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
D18V6, 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)                 35
  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    22
D18V7, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    2                 16
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    7                 22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    5  4
  11P GAIN WILD-TYPE  7 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5    4
  11P GAIN WILD-TYPE    7   32
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                  7
  NOT HISPANIC OR LATINO                4                 32
[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 27  7
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                13                 34 
  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        32.28       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        24.62        23.64         8.15 
TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       18.18        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        70.06       211.23        19.56       116.81       196.60 
TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       51.98        43.86        38.24       128.12        24.00        53.16 
TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-RQ-A6JB 
       45.14        25.15       111.58         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 
             32.28              25.58 
[1] "0.6 - 150.5 (32.3)" "0.0 - 211.2 (25.6)"
[1] "hr=" "1.2"
D19V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  11Q GAIN MUTATED         0                  0    1     2      0     1     0
  11Q GAIN WILD-TYPE       2                  2    3     1      1     1     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  11Q GAIN MUTATED                       0             0               2
  11Q GAIN WILD-TYPE                     1             1               1
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  11Q GAIN MUTATED                                               1       0
  11Q GAIN WILD-TYPE                                             0       2
                    vv
clus                 THYROID
  11Q GAIN MUTATED         1
  11Q GAIN WILD-TYPE       1
D19V3, multiclass
                                               clus
vv                                              11Q GAIN MUTATED
  ADRENAL                                                      0
  ASCITES/PERITONEUM                                           0
  BONE                                                         1
  BRAIN                                                        2
  BREAST                                                       0
  COLON                                                        1
  LIVER                                                        0
  OTHER EXTRANODAL SITE                                        0
  PAROTID GLAND                                                0
  SMALL INTESTINE                                              2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                1
  STOMACH                                                      0
  THYROID                                                      1
                                               clus
vv                                              11Q GAIN WILD-TYPE
  ADRENAL                                                        2
  ASCITES/PERITONEUM                                             2
  BONE                                                           3
  BRAIN                                                          1
  BREAST                                                         1
  COLON                                                          1
  LIVER                                                          1
  OTHER EXTRANODAL SITE                                          1
  PAROTID GLAND                                                  1
  SMALL INTESTINE                                                1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                  0
  STOMACH                                                        2
  THYROID                                                        1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V4, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED   10  3
  11Q GAIN WILD-TYPE 16 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     10    3
  11Q GAIN WILD-TYPE   16   19
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               10                 16
  MALE                  3                 19
[1] 2 2
[1] FALSE
D19V5, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED   12  1
  11Q GAIN WILD-TYPE 28  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     12    1
  11Q GAIN WILD-TYPE   28    6
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                12                 28
  YES                1                  6
[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                                                                                31
                    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
D19V6, 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)                 31
  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    20
D19V7, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    4                 14
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    9                 20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    5  8
  11Q GAIN WILD-TYPE  7 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5    8
  11Q GAIN WILD-TYPE    7   28
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                  7
  NOT HISPANIC OR LATINO                8                 28
[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 33  7
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 7                 40 
  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        25.15 
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        24.62        23.64        14.04 
TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       18.18        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        70.06       211.23        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 
      196.60       150.51        98.07        51.98        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       32.28       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      111.58        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 
            25.150             29.225 
[1] "0.6 - 42.7 (25.1)"  "0.0 - 211.2 (29.2)"
[1] "hr=" "2.7"
D20V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  12P GAIN MUTATED         0                  0    2     1      0     0     0
  12P GAIN WILD-TYPE       2                  2    2     2      1     2     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  12P GAIN MUTATED                       0             0               1
  12P GAIN WILD-TYPE                     1             1               2
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  12P GAIN MUTATED                                               0       0
  12P GAIN WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  12P GAIN MUTATED         0
  12P GAIN WILD-TYPE       2
D20V3, multiclass
                                               clus
vv                                              12P GAIN MUTATED
  ADRENAL                                                      0
  ASCITES/PERITONEUM                                           0
  BONE                                                         2
  BRAIN                                                        1
  BREAST                                                       0
  COLON                                                        0
  LIVER                                                        0
  OTHER EXTRANODAL SITE                                        0
  PAROTID GLAND                                                0
  SMALL INTESTINE                                              1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                0
  STOMACH                                                      0
  THYROID                                                      0
                                               clus
vv                                              12P GAIN WILD-TYPE
  ADRENAL                                                        2
  ASCITES/PERITONEUM                                             2
  BONE                                                           2
  BRAIN                                                          2
  BREAST                                                         1
  COLON                                                          2
  LIVER                                                          1
  OTHER EXTRANODAL SITE                                          1
  PAROTID GLAND                                                  1
  SMALL INTESTINE                                                2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                  1
  STOMACH                                                        2
  THYROID                                                        2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V4, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    4  3
  12P GAIN WILD-TYPE 22 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      4    3
  12P GAIN WILD-TYPE   22   19
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                4                 22
  MALE                  3                 19
[1] 2 2
[1] FALSE
D20V5, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    5  2
  12P GAIN WILD-TYPE 35  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      5    2
  12P GAIN WILD-TYPE   35    5
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 5                 35
  YES                2                  5
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  12P GAIN MUTATED                                                                                   4
  12P GAIN WILD-TYPE                                                                                37
                    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
D20V6, 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)                 37
  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    25
D20V7, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    4                 25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    3  4
  12P GAIN WILD-TYPE  9 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3    4
  12P GAIN WILD-TYPE    9   32
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  9
  NOT HISPANIC OR LATINO                4                 32
[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 32  6
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 9                 38 
  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 
       25.15        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        24.62        23.64        14.04 
TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       18.18        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
       22.32         9.80        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        70.06       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        51.98        43.86        57.17        32.28 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9U3 
      128.12        24.00        53.16        45.14       109.58       111.58 
TCGA-GS-A9U4 TCGA-RQ-A6JB 
       12.85         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 
            25.150             31.415 
[1] "0.6 - 42.7 (25.1)"  "0.0 - 211.2 (31.4)"
[1] "hr=" "4"  
D21V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  12Q GAIN MUTATED         0                  0    2     3      0     0     0
  12Q GAIN WILD-TYPE       2                  2    2     0      1     2     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  12Q GAIN MUTATED                       0             0               1
  12Q GAIN WILD-TYPE                     1             1               2
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  12Q GAIN MUTATED                                               0       0
  12Q GAIN WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  12Q GAIN MUTATED         0
  12Q GAIN WILD-TYPE       2
D21V3, multiclass
                                               clus
vv                                              12Q GAIN MUTATED
  ADRENAL                                                      0
  ASCITES/PERITONEUM                                           0
  BONE                                                         2
  BRAIN                                                        3
  BREAST                                                       0
  COLON                                                        0
  LIVER                                                        0
  OTHER EXTRANODAL SITE                                        0
  PAROTID GLAND                                                0
  SMALL INTESTINE                                              1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                0
  STOMACH                                                      0
  THYROID                                                      0
                                               clus
vv                                              12Q GAIN WILD-TYPE
  ADRENAL                                                        2
  ASCITES/PERITONEUM                                             2
  BONE                                                           2
  BRAIN                                                          0
  BREAST                                                         1
  COLON                                                          2
  LIVER                                                          1
  OTHER EXTRANODAL SITE                                          1
  PAROTID GLAND                                                  1
  SMALL INTESTINE                                                2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                  1
  STOMACH                                                        2
  THYROID                                                        2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V4, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    4  5
  12Q GAIN WILD-TYPE 22 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4    5
  12Q GAIN WILD-TYPE   22   17
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                4                 22
  MALE                  5                 17
[1] 2 2
[1] FALSE
D21V5, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    7  2
  12Q GAIN WILD-TYPE 33  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      7    2
  12Q GAIN WILD-TYPE   33    5
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 7                 33
  YES                2                  5
[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                                                                                36
                    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
D21V6, 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)                 36
  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    24
D21V7, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    4                 14
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    5                 24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    4  5
  12Q GAIN WILD-TYPE  8 31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4    5
  12Q GAIN WILD-TYPE    8   31
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  8
  NOT HISPANIC OR LATINO                5                 31
[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 34  8
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                 42 
  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 
       24.62        24.69        12.66        32.28        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        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 
       14.04        18.18        35.54        31.10        31.73         4.14 
TCGA-FF-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-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        70.06       211.23        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        98.07        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       57.17        38.24       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
      109.58        25.15       111.58        25.91         0.03         0.56 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             12.66               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             32.28             211.23 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            24.620             31.415 
[1] "12.7 - 32.3 (24.6)" "0.0 - 211.2 (31.4)"
[1] "hr=" "1.6"
D22V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  13Q GAIN MUTATED         1                  0    0     0      0     0     0
  13Q GAIN WILD-TYPE       1                  2    4     3      1     2     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  13Q GAIN MUTATED                       0             0               0
  13Q GAIN WILD-TYPE                     1             1               3
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  13Q GAIN MUTATED                                               0       0
  13Q GAIN WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  13Q GAIN MUTATED         0
  13Q GAIN WILD-TYPE       2
D22V3, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                 24 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FA-A7DS         TCGA-FA-A82F         TCGA-FF-8043 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FF-8061         TCGA-FF-8062         TCGA-FF-A7CQ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FF-A7CR         TCGA-FF-A7CW         TCGA-FM-8000 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G8-6324         TCGA-G8-6326         TCGA-G8-6906 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-A4D4         TCGA-GR-A4D5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GR-A4D9         TCGA-GS-A9TT         TCGA-RQ-A68N 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-RQ-A6JB         TCGA-RQ-AAAT         TCGA-VB-A8QN 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D22V4, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    3  2
  13Q GAIN WILD-TYPE 23 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3    2
  13Q GAIN WILD-TYPE   23   20
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                3                 23
  MALE                  2                 20
[1] 2 2
[1] FALSE
D22V5, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    5  0
  13Q GAIN WILD-TYPE 35  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5    0
  13Q GAIN WILD-TYPE   35    7
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 5                 35
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  13Q GAIN MUTATED                                                                                   5
  13Q GAIN WILD-TYPE                                                                                36
                    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
D22V6, 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)                 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
  13Q GAIN MUTATED       3                         0     2
  13Q GAIN WILD-TYPE    15                         1    27
D22V7, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    2  3
  13Q GAIN WILD-TYPE 10 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2    3
  13Q GAIN WILD-TYPE   10   33
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                3                 33
[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 33  7
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                 40 
  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        51.98        25.15 
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-FA-A86F 
        4.34         4.34         1.91        24.62        23.64        18.18 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       35.54        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-G8-6324 
       22.32         9.80        10.29        26.01        12.66        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        70.06       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        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB TCGA-RQ-AAAT 
      111.58        12.85         0.03         0.56 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              8.15               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             51.98             211.23 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            25.150             31.415 
[1] "8.2 - 52.0 (25.1)"  "0.0 - 211.2 (31.4)"
[1] "hr=" "2.4"
D23V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  16P GAIN MUTATED         0                  0    1     1      0     1     0
  16P GAIN WILD-TYPE       2                  2    3     2      1     1     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  16P GAIN MUTATED                       0             0               2
  16P GAIN WILD-TYPE                     1             1               1
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  16P GAIN MUTATED                                               0       0
  16P GAIN WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  16P GAIN MUTATED         0
  16P GAIN WILD-TYPE       2
D23V3, multiclass
                                               clus
vv                                              16P GAIN MUTATED
  ADRENAL                                                      0
  ASCITES/PERITONEUM                                           0
  BONE                                                         1
  BRAIN                                                        1
  BREAST                                                       0
  COLON                                                        1
  LIVER                                                        0
  OTHER EXTRANODAL SITE                                        0
  PAROTID GLAND                                                0
  SMALL INTESTINE                                              2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                0
  STOMACH                                                      0
  THYROID                                                      0
                                               clus
vv                                              16P GAIN WILD-TYPE
  ADRENAL                                                        2
  ASCITES/PERITONEUM                                             2
  BONE                                                           3
  BRAIN                                                          2
  BREAST                                                         1
  COLON                                                          1
  LIVER                                                          1
  OTHER EXTRANODAL SITE                                          1
  PAROTID GLAND                                                  1
  SMALL INTESTINE                                                1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                  1
  STOMACH                                                        2
  THYROID                                                        2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V4, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    4  3
  16P GAIN WILD-TYPE 22 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4    3
  16P GAIN WILD-TYPE   22   19
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                4                 22
  MALE                  3                 19
[1] 2 2
[1] FALSE
D23V5, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    6  1
  16P GAIN WILD-TYPE 34  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      6    1
  16P GAIN WILD-TYPE   34    6
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 6                 34
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  16P GAIN MUTATED                                                                                   5
  16P GAIN WILD-TYPE                                                                                36
                    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
D23V6, 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)                 36
  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    25
D23V7, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    4                 25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    2  5
  16P GAIN WILD-TYPE 10 31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2    5
  16P GAIN WILD-TYPE   10   31
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                5                 31
[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 34  6
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                 40 
  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        25.15 
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-FA-A86F 
        4.34         4.34         1.91        24.62        23.64        18.18 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       35.54        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-G8-6324 
       22.32         9.80        10.29        26.01        12.66        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7351 
       51.98        70.06       211.23        19.56       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       98.07        51.98        42.71        43.86        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB TCGA-RQ-AAAT 
      111.58        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 
            25.150             31.415 
[1] "8.2 - 116.8 (25.1)" "0.0 - 211.2 (31.4)"
[1] "hr=" "3.5"
D24V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  16Q GAIN MUTATED         0                  0    0     1      0     1     0
  16Q GAIN WILD-TYPE       2                  2    4     2      1     1     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  16Q GAIN MUTATED                       0             0               2
  16Q GAIN WILD-TYPE                     1             1               1
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  16Q GAIN MUTATED                                               0       0
  16Q GAIN WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  16Q GAIN MUTATED         0
  16Q GAIN WILD-TYPE       2
D24V3, multiclass
                                               clus
vv                                              16Q GAIN MUTATED
  ADRENAL                                                      0
  ASCITES/PERITONEUM                                           0
  BONE                                                         0
  BRAIN                                                        1
  BREAST                                                       0
  COLON                                                        1
  LIVER                                                        0
  OTHER EXTRANODAL SITE                                        0
  PAROTID GLAND                                                0
  SMALL INTESTINE                                              2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                0
  STOMACH                                                      0
  THYROID                                                      0
                                               clus
vv                                              16Q GAIN WILD-TYPE
  ADRENAL                                                        2
  ASCITES/PERITONEUM                                             2
  BONE                                                           4
  BRAIN                                                          2
  BREAST                                                         1
  COLON                                                          1
  LIVER                                                          1
  OTHER EXTRANODAL SITE                                          1
  PAROTID GLAND                                                  1
  SMALL INTESTINE                                                1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                  1
  STOMACH                                                        2
  THYROID                                                        2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V4, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3  4
  16Q GAIN WILD-TYPE 23 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3    4
  16Q GAIN WILD-TYPE   23   18
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                3                 23
  MALE                  4                 18
[1] 2 2
[1] FALSE
D24V5, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    6  1
  16Q GAIN WILD-TYPE 34  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      6    1
  16Q GAIN WILD-TYPE   34    6
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 6                 34
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  16Q GAIN MUTATED                                                                                   5
  16Q GAIN WILD-TYPE                                                                                36
                    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
D24V6, 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)                 36
  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    25
D24V7, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    4                 25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    2  5
  16Q GAIN WILD-TYPE 10 31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2    5
  16Q GAIN WILD-TYPE   10   31
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                5                 31
[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 36  8
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                 44 
  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        24.62        23.64 
TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       18.18        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        70.06       211.23        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        98.07        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       57.17        32.28        38.24       128.12        24.00        53.16 
TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N 
       45.14       109.58        25.15       111.58        12.85        25.91 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         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 
            14.040             29.225 
[1] "8.2 - 35.5 (14.0)"  "0.0 - 211.2 (29.2)"
[1] "hr=" "3.8"
D25V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  17Q GAIN MUTATED         0                  0    0     0      0     0     0
  17Q GAIN WILD-TYPE       2                  2    4     3      1     2     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  17Q GAIN MUTATED                       0             0               1
  17Q GAIN WILD-TYPE                     1             1               2
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  17Q GAIN MUTATED                                               0       0
  17Q GAIN WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  17Q GAIN MUTATED         0
  17Q GAIN WILD-TYPE       2
D25V3, multiclass
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                 24 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FA-A7DS         TCGA-FF-8043         TCGA-FF-8061 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FF-A7CQ         TCGA-FF-A7CR 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FF-A7CW         TCGA-FF-A7CX         TCGA-FM-8000 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G8-6324         TCGA-G8-6326         TCGA-G8-6906 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-A4D4         TCGA-GR-A4D5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GR-A4D9         TCGA-GS-A9TT         TCGA-RQ-A68N 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-RQ-A6JB         TCGA-RQ-AAAT         TCGA-VB-A8QN 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
D25V4, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    3  0
  17Q GAIN WILD-TYPE 23 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3    0
  17Q GAIN WILD-TYPE   23   22
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                3                 23
  MALE                  0                 22
[1] 2 2
[1] FALSE
D25V5, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    3  0
  17Q GAIN WILD-TYPE 37  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3    0
  17Q GAIN WILD-TYPE   37    7
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 3                 37
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  17Q GAIN MUTATED                                                                                   2
  17Q GAIN WILD-TYPE                                                                                39
                    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
D25V6, 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)                 39
  PRIMARY DLBCL OF THE CNS                                                                           3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       3                         0     0
  17Q GAIN WILD-TYPE    15                         1    29
D25V7, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    0                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    0  3
  17Q GAIN WILD-TYPE 12 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0    3
  17Q GAIN WILD-TYPE   12   33
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                3                 33
[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 25  9
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                13                 34 
  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 
       24.62        23.64        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       128.12        53.16 
TCGA-GS-A9U3 
      111.58 

$`18P GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7Q1 TCGA-FA-A86F 
        4.34         4.34        23.28         1.91         8.15        18.18 
TCGA-FF-8041 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CR 
       35.54        24.69         4.14        27.35        22.32        10.29 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       12.66        31.96        41.16        51.98        70.06       211.23 
TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
       19.56       116.81       150.51        98.07        51.98        42.71 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
       57.17        32.28        24.00        45.14       109.58        25.15 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85        25.91         0.03         0.56 

  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              25.53 
[1] "9.8 - 196.6 (31.7)" "0.0 - 211.2 (25.5)"
[1] "hr="     "3.4e+08"
D26V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  18P GAIN MUTATED         1                  0    1     0      1     1     0
  18P GAIN WILD-TYPE       1                  2    3     3      0     1     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  18P GAIN MUTATED                       0             1               1
  18P GAIN WILD-TYPE                     1             0               2
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  18P GAIN MUTATED                                               0       0
  18P GAIN WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  18P GAIN MUTATED         0
  18P GAIN WILD-TYPE       2
D26V3, multiclass
                                               clus
vv                                              18P GAIN MUTATED
  ADRENAL                                                      1
  ASCITES/PERITONEUM                                           0
  BONE                                                         1
  BRAIN                                                        0
  BREAST                                                       1
  COLON                                                        1
  LIVER                                                        0
  OTHER EXTRANODAL SITE                                        0
  PAROTID GLAND                                                1
  SMALL INTESTINE                                              1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                0
  STOMACH                                                      0
  THYROID                                                      0
                                               clus
vv                                              18P GAIN WILD-TYPE
  ADRENAL                                                        1
  ASCITES/PERITONEUM                                             2
  BONE                                                           3
  BRAIN                                                          3
  BREAST                                                         0
  COLON                                                          1
  LIVER                                                          1
  OTHER EXTRANODAL SITE                                          1
  PAROTID GLAND                                                  0
  SMALL INTESTINE                                                2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                  1
  STOMACH                                                        2
  THYROID                                                        2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V4, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    8  5
  18P GAIN WILD-TYPE 18 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      8    5
  18P GAIN WILD-TYPE   18   17
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                8                 18
  MALE                  5                 17
[1] 2 2
[1] FALSE
D26V5, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   10  3
  18P GAIN WILD-TYPE 30  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     10    3
  18P GAIN WILD-TYPE   30    4
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                10                 30
  YES                3                  4
[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                                                                                29
                    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
D26V6, 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)                 29
  PRIMARY DLBCL OF THE CNS                                                                           3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       8                         0     5
  18P GAIN WILD-TYPE    10                         1    24
D26V7, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    8                 10
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    5                 24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    4  9
  18P GAIN WILD-TYPE  8 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4    9
  18P GAIN WILD-TYPE    8   27
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  8
  NOT HISPANIC OR LATINO                9                 27
[1] 2 2
[1] FALSE

Clustering(27) Variable = 18Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED   13  0
  18Q GAIN WILD-TYPE 25  9
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                13                 34 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                  9 
$`18Q GAIN MUTATED`
TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-A7CQ 
       24.62        23.64        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       128.12        53.16 
TCGA-GS-A9U3 
      111.58 

$`18Q GAIN WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7Q1 TCGA-FA-A86F 
        4.34         4.34        23.28         1.91         8.15        18.18 
TCGA-FF-8041 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CR 
       35.54        24.69         4.14        27.35        22.32        10.29 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       12.66        31.96        41.16        51.98        70.06       211.23 
TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
       19.56       116.81       150.51        98.07        51.98        42.71 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
       57.17        32.28        24.00        45.14       109.58        25.15 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85        25.91         0.03         0.56 

  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 
             31.73              25.53 
[1] "9.8 - 196.6 (31.7)" "0.0 - 211.2 (25.5)"
[1] "hr="     "3.4e+08"
D27V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  18Q GAIN MUTATED         1                  0    1     0      1     1     0
  18Q GAIN WILD-TYPE       1                  2    3     3      0     1     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  18Q GAIN MUTATED                       0             1               1
  18Q GAIN WILD-TYPE                     1             0               2
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  18Q GAIN MUTATED                                               0       0
  18Q GAIN WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  18Q GAIN MUTATED         0
  18Q GAIN WILD-TYPE       2
D27V3, multiclass
                                               clus
vv                                              18Q GAIN MUTATED
  ADRENAL                                                      1
  ASCITES/PERITONEUM                                           0
  BONE                                                         1
  BRAIN                                                        0
  BREAST                                                       1
  COLON                                                        1
  LIVER                                                        0
  OTHER EXTRANODAL SITE                                        0
  PAROTID GLAND                                                1
  SMALL INTESTINE                                              1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                0
  STOMACH                                                      0
  THYROID                                                      0
                                               clus
vv                                              18Q GAIN WILD-TYPE
  ADRENAL                                                        1
  ASCITES/PERITONEUM                                             2
  BONE                                                           3
  BRAIN                                                          3
  BREAST                                                         0
  COLON                                                          1
  LIVER                                                          1
  OTHER EXTRANODAL SITE                                          1
  PAROTID GLAND                                                  0
  SMALL INTESTINE                                                2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                  1
  STOMACH                                                        2
  THYROID                                                        2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V4, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    8  5
  18Q GAIN WILD-TYPE 18 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      8    5
  18Q GAIN WILD-TYPE   18   17
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                8                 18
  MALE                  5                 17
[1] 2 2
[1] FALSE
D27V5, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED   10  3
  18Q GAIN WILD-TYPE 30  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     10    3
  18Q GAIN WILD-TYPE   30    4
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                10                 30
  YES                3                  4
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  18Q GAIN MUTATED                                                                                  12
  18Q GAIN WILD-TYPE                                                                                29
                    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
D27V6, multiclass
                                                                                   clus
vv                                                                                  18Q 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                                                                                  18Q GAIN WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                 29
  PRIMARY DLBCL OF THE CNS                                                                           3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       8                         0     5
  18Q GAIN WILD-TYPE    10                         1    24
D27V7, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    8                 10
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    5                 24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    4  9
  18Q GAIN WILD-TYPE  8 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    9
  18Q GAIN WILD-TYPE    8   27
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  8
  NOT HISPANIC OR LATINO                9                 27
[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 35  9
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                 44 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 0                  9 
$`19P GAIN MUTATED`
TCGA-FA-A6HO TCGA-GS-A9TT TCGA-GS-A9TY 
       24.62        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        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       12.66        31.96        41.16        51.98        70.06       211.23 
TCGA-G8-6907 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        51.98 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TU TCGA-GS-A9TV 
       42.71        43.86        57.17        32.28       128.12        24.00 
TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N 
       53.16        45.14        25.15       111.58        12.85        25.91 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             24.62               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            109.58             211.23 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             38.24              26.68 
[1] "24.6 - 109.6 (38.2)" "0.0 - 211.2 (26.7)" 
[1] "hr="     "7.5e+07"
D28V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  19P GAIN MUTATED         0                  0    1     0      0     0     0
  19P GAIN WILD-TYPE       2                  2    3     3      1     2     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  19P GAIN MUTATED                       0             0               0
  19P GAIN WILD-TYPE                     1             1               3
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  19P GAIN MUTATED                                               0       0
  19P GAIN WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  19P GAIN MUTATED         0
  19P GAIN WILD-TYPE       2
D28V3, multiclass
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 1                 24 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FA-A7DS         TCGA-FA-A82F         TCGA-FF-8043 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FF-8061         TCGA-FF-8062         TCGA-FF-A7CQ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FF-A7CR         TCGA-FF-A7CW         TCGA-FF-A7CX 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6326 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G8-6906         TCGA-GR-7351         TCGA-GR-A4D4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D9         TCGA-RQ-A68N 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-RQ-A6JB         TCGA-RQ-AAAT         TCGA-VB-A8QN 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
D28V4, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    2  1
  19P GAIN WILD-TYPE 24 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2    1
  19P GAIN WILD-TYPE   24   21
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                2                 24
  MALE                  1                 21
[1] 2 2
[1] FALSE
D28V5, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    2  1
  19P GAIN WILD-TYPE 38  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2    1
  19P GAIN WILD-TYPE   38    6
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 2                 38
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  19P GAIN MUTATED                                                                                   3
  19P GAIN WILD-TYPE                                                                                38
                    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
D28V6, 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)                 38
  PRIMARY DLBCL OF THE CNS                                                                           3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       1                         0     2
  19P GAIN WILD-TYPE    17                         1    27
D28V7, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    1                 17
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    2  1
  19P GAIN WILD-TYPE 10 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2    1
  19P GAIN WILD-TYPE   10   35
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                1                 35
[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 35  9
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                 44 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 0                  9 
$`19Q GAIN MUTATED`
TCGA-FA-A6HO TCGA-GS-A9TT TCGA-GS-A9TY 
       24.62        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        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       12.66        31.96        41.16        51.98        70.06       211.23 
TCGA-G8-6907 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        51.98 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TU TCGA-GS-A9TV 
       42.71        43.86        57.17        32.28       128.12        24.00 
TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N 
       53.16        45.14        25.15       111.58        12.85        25.91 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             24.62               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            109.58             211.23 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             38.24              26.68 
[1] "24.6 - 109.6 (38.2)" "0.0 - 211.2 (26.7)" 
[1] "hr="     "7.5e+07"
D29V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  19Q GAIN MUTATED         0                  0    1     0      0     0     0
  19Q GAIN WILD-TYPE       2                  2    3     3      1     2     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  19Q GAIN MUTATED                       0             0               0
  19Q GAIN WILD-TYPE                     1             1               3
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  19Q GAIN MUTATED                                               0       0
  19Q GAIN WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  19Q GAIN MUTATED         0
  19Q GAIN WILD-TYPE       2
D29V3, multiclass
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 1                 24 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FA-A7DS         TCGA-FA-A82F         TCGA-FF-8043 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FF-8061         TCGA-FF-8062         TCGA-FF-A7CQ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FF-A7CR         TCGA-FF-A7CW         TCGA-FF-A7CX 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6326 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G8-6906         TCGA-GR-7351         TCGA-GR-A4D4 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D9         TCGA-RQ-A68N 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-RQ-A6JB         TCGA-RQ-AAAT         TCGA-VB-A8QN 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
D29V4, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    2  1
  19Q GAIN WILD-TYPE 24 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2    1
  19Q GAIN WILD-TYPE   24   21
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                2                 24
  MALE                  1                 21
[1] 2 2
[1] FALSE
D29V5, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    2  1
  19Q GAIN WILD-TYPE 38  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2    1
  19Q GAIN WILD-TYPE   38    6
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 2                 38
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  19Q GAIN MUTATED                                                                                   3
  19Q GAIN WILD-TYPE                                                                                38
                    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
D29V6, 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)                 38
  PRIMARY DLBCL OF THE CNS                                                                           3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       1                         0     2
  19Q GAIN WILD-TYPE    17                         1    27
D29V7, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    1                 17
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V8, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    2  1
  19Q GAIN WILD-TYPE 10 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2    1
  19Q GAIN WILD-TYPE   10   35
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                1                 35
[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 34  8
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 5                 42 
  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        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
        8.15        18.18        31.10        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        70.06       211.23        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        98.07        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       57.17        32.28        38.24       128.12        24.00        53.16 
TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       45.14        25.15       111.58        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              26.68 
[1] "12.8 - 109.6 (31.7)" "0.0 - 211.2 (26.7)" 
[1] "hr=" "1.4"
D30V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  20P GAIN MUTATED         0                  0    0     0      0     1     0
  20P GAIN WILD-TYPE       2                  2    4     3      1     1     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  20P GAIN MUTATED                       0             0               1
  20P GAIN WILD-TYPE                     1             1               2
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  20P GAIN MUTATED                                               0       0
  20P GAIN WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  20P GAIN MUTATED         0
  20P GAIN WILD-TYPE       2
D30V3, multiclass
[1] "Remove cluster labels:" "20P GAIN MUTATED"      
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                 23 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FA-A7DS         TCGA-FF-8061         TCGA-FF-8062 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FF-A7CQ         TCGA-FF-A7CR         TCGA-FF-A7CW 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FF-A7CX         TCGA-FM-8000         TCGA-G8-6324 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-GR-7351 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GR-A4D4         TCGA-GR-A4D5         TCGA-GR-A4D9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GS-A9TT         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-RQ-AAAT         TCGA-VB-A8QN 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
D30V4, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    5  0
  20P GAIN WILD-TYPE 21 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      5    0
  20P GAIN WILD-TYPE   21   22
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                5                 21
  MALE                  0                 22
[1] 2 2
[1] FALSE
D30V5, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    5  0
  20P GAIN WILD-TYPE 35  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      5    0
  20P GAIN WILD-TYPE   35    7
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 5                 35
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  20P GAIN MUTATED                                                                                   4
  20P GAIN WILD-TYPE                                                                                37
                    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
D30V6, 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)                 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
  20P GAIN MUTATED       3                         0     2
  20P GAIN WILD-TYPE    15                         1    27
D30V7, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    2  3
  20P GAIN WILD-TYPE 10 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2    3
  20P GAIN WILD-TYPE   10   33
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                3                 33
[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 35  8
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 4                 43 
  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        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
        8.15        18.18        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       31.96        41.16        51.98        70.06       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
      116.81       196.60       150.51        98.07        51.98        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV 
       43.86        57.17        32.28        38.24       128.12        24.00 
TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-RQ-A68N TCGA-RQ-A6JB 
       53.16        45.14        25.15       111.58        25.91         0.03 
TCGA-RQ-AAAT 
        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 
             24.79              27.35 
[1] "12.8 - 109.6 (24.8)" "0.0 - 211.2 (27.4)" 
[1] "hr=" "1.9"
D31V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  20Q GAIN MUTATED         0                  0    0     0      0     0     0
  20Q GAIN WILD-TYPE       2                  2    4     3      1     2     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  20Q GAIN MUTATED                       0             0               1
  20Q GAIN WILD-TYPE                     1             1               2
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  20Q GAIN MUTATED                                               0       0
  20Q GAIN WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  20Q GAIN MUTATED         0
  20Q GAIN WILD-TYPE       2
D31V3, multiclass
[1] "Remove cluster labels:" "20Q GAIN MUTATED"      
clus
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 1                 24 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FA-A7DS         TCGA-FF-8043         TCGA-FF-8061 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FF-8062         TCGA-FF-A7CQ         TCGA-FF-A7CR 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FF-A7CW         TCGA-FF-A7CX         TCGA-FM-8000 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G8-6324         TCGA-G8-6326         TCGA-G8-6906 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-A4D4         TCGA-GR-A4D5 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GR-A4D9         TCGA-GS-A9TT         TCGA-RQ-A68N 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-RQ-A6JB         TCGA-RQ-AAAT         TCGA-VB-A8QN 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
D31V4, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    4  0
  20Q GAIN WILD-TYPE 22 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4    0
  20Q GAIN WILD-TYPE   22   22
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                4                 22
  MALE                  0                 22
[1] 2 2
[1] FALSE
D31V5, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    4  0
  20Q GAIN WILD-TYPE 36  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4    0
  20Q GAIN WILD-TYPE   36    7
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 4                 36
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  20Q GAIN MUTATED                                                                                   3
  20Q GAIN WILD-TYPE                                                                                38
                    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
D31V6, 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)                 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
  20Q GAIN MUTATED       2                         0     2
  20Q GAIN WILD-TYPE    16                         1    27
D31V7, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    2                 16
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    2                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    2  2
  20Q GAIN WILD-TYPE 10 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2    2
  20Q GAIN WILD-TYPE   10   34
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                2                 34
[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 30  7
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                 37 
  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        53.16       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        24.62        23.64         8.15 
TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       18.18        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-G8-6914 TCGA-GR-A4D4 
       51.98        70.06       211.23        19.56       196.60        51.98 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU 
       42.71        43.86        57.17        32.28        38.24       128.12 
TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-RQ-A68N TCGA-RQ-A6JB 
       24.00        45.14        25.15       111.58        25.91         0.03 
TCGA-RQ-AAAT 
        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 
             44.35              25.91 
[1] "4.3 - 150.5 (44.3)" "0.0 - 211.2 (25.9)"
[1] "hr=" "1"  
D32V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  21Q GAIN MUTATED         0                  0    0     0      0     1     1
  21Q GAIN WILD-TYPE       2                  2    4     3      1     1     0
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  21Q GAIN MUTATED                       0             0               1
  21Q GAIN WILD-TYPE                     1             1               2
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  21Q GAIN MUTATED                                               0       0
  21Q GAIN WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  21Q GAIN MUTATED         1
  21Q GAIN WILD-TYPE       1
D32V3, multiclass
                                               clus
vv                                              21Q GAIN MUTATED
  ADRENAL                                                      0
  ASCITES/PERITONEUM                                           0
  BONE                                                         0
  BRAIN                                                        0
  BREAST                                                       0
  COLON                                                        1
  LIVER                                                        1
  OTHER EXTRANODAL SITE                                        0
  PAROTID GLAND                                                0
  SMALL INTESTINE                                              1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                0
  STOMACH                                                      0
  THYROID                                                      1
                                               clus
vv                                              21Q GAIN WILD-TYPE
  ADRENAL                                                        2
  ASCITES/PERITONEUM                                             2
  BONE                                                           4
  BRAIN                                                          3
  BREAST                                                         1
  COLON                                                          1
  LIVER                                                          0
  OTHER EXTRANODAL SITE                                          1
  PAROTID GLAND                                                  1
  SMALL INTESTINE                                                2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                  1
  STOMACH                                                        2
  THYROID                                                        1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V4, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    7  3
  21Q GAIN WILD-TYPE 19 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      7    3
  21Q GAIN WILD-TYPE   19   19
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                7                 19
  MALE                  3                 19
[1] 2 2
[1] FALSE
D32V5, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    8  2
  21Q GAIN WILD-TYPE 32  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      8    2
  21Q GAIN WILD-TYPE   32    5
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 8                 32
  YES                2                  5
[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                                                                                33
                    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
D32V6, 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)                 33
  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    22
D32V7, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    7                 22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    3  7
  21Q GAIN WILD-TYPE  9 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    7
  21Q GAIN WILD-TYPE    9   29
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  9
  NOT HISPANIC OR LATINO                7                 29
[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 33  8
  XP GAIN MUTATED XP GAIN WILD-TYPE 
                6                41 
  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        53.16       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        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CX 
        4.14        27.35        22.32         9.80        10.29        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       31.96        41.16        51.98        70.06       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
      116.81       196.60       150.51        98.07        51.98        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV 
       43.86        57.17        32.28        38.24       128.12        24.00 
TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB 
       45.14        25.15       111.58        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 
            25.96             31.10 
[1] "0.6 - 109.6 (26.0)" "0.0 - 211.2 (31.1)"
[1] "hr=" "1.1"
D33V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  XP GAIN MUTATED         0                  0    0     2      0     0     0
  XP GAIN WILD-TYPE       2                  2    4     1      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  XP GAIN MUTATED                       0             1               1
  XP GAIN WILD-TYPE                     1             0               2
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  XP GAIN MUTATED                                               0       0
  XP GAIN WILD-TYPE                                             1       2
                   vv
clus                THYROID
  XP GAIN MUTATED         0
  XP GAIN WILD-TYPE       2
D33V3, multiclass
                                               clus
vv                                              XP GAIN MUTATED
  ADRENAL                                                     0
  ASCITES/PERITONEUM                                          0
  BONE                                                        0
  BRAIN                                                       2
  BREAST                                                      0
  COLON                                                       0
  LIVER                                                       0
  OTHER EXTRANODAL SITE                                       0
  PAROTID GLAND                                               1
  SMALL INTESTINE                                             1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)               0
  STOMACH                                                     0
  THYROID                                                     0
                                               clus
vv                                              XP GAIN WILD-TYPE
  ADRENAL                                                       2
  ASCITES/PERITONEUM                                            2
  BONE                                                          4
  BRAIN                                                         1
  BREAST                                                        1
  COLON                                                         2
  LIVER                                                         1
  OTHER EXTRANODAL SITE                                         1
  PAROTID GLAND                                                 0
  SMALL INTESTINE                                               2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                 1
  STOMACH                                                       2
  THYROID                                                       2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V4, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    3  3
  XP GAIN WILD-TYPE 23 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      3    3
  XP GAIN WILD-TYPE   23   19
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE               3                23
  MALE                 3                19
[1] 2 2
[1] FALSE
D33V5, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    5  1
  XP GAIN WILD-TYPE 35  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      5    1
  XP GAIN WILD-TYPE   35    6
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO                5                35
  YES               1                 6
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  XP GAIN MUTATED                                                                                   3
  XP GAIN WILD-TYPE                                                                                38
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  XP GAIN MUTATED                          2                                  1
  XP GAIN WILD-TYPE                        1                                  3
D33V6, 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)                38
  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    25
D33V7, multiclass
                           clus
vv                          XP GAIN MUTATED XP GAIN WILD-TYPE
  ASIAN                                   2                16
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   4                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, binary
                   cls
clus                 0  1
  XP GAIN MUTATED    4  2
  XP GAIN WILD-TYPE  8 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      4    2
  XP GAIN WILD-TYPE    8   34
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 8
  NOT HISPANIC OR LATINO               2                34
[1] 2 2
[1] FALSE

Clustering(34) Variable = XQ GAIN MUTATION ANALYSIS
D34V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED    6  1
  XQ GAIN WILD-TYPE 32  8
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                7                40 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                 8 
$`XQ GAIN MUTATED`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-A7CW TCGA-GS-A9TY TCGA-GS-A9U3 TCGA-RQ-A68N 
       23.28        35.54        26.01       109.58       111.58        25.91 
TCGA-RQ-AAAT 
        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        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       14.04        18.18        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-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        70.06       211.23        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        98.07        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       57.17        32.28        38.24       128.12        24.00        53.16 
TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U4 TCGA-RQ-A6JB 
       45.14        25.15        12.85         0.03 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.56              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           111.58            211.23 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           26.010            29.225 
[1] "0.6 - 111.6 (26.0)" "0.0 - 211.2 (29.2)"
[1] "hr=" "1.1"
D34V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  XQ GAIN MUTATED         0                  0    0     2      0     0     0
  XQ GAIN WILD-TYPE       2                  2    4     1      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  XQ GAIN MUTATED                       0             1               1
  XQ GAIN WILD-TYPE                     1             0               2
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  XQ GAIN MUTATED                                               0       0
  XQ GAIN WILD-TYPE                                             1       2
                   vv
clus                THYROID
  XQ GAIN MUTATED         0
  XQ GAIN WILD-TYPE       2
D34V3, multiclass
                                               clus
vv                                              XQ GAIN MUTATED
  ADRENAL                                                     0
  ASCITES/PERITONEUM                                          0
  BONE                                                        0
  BRAIN                                                       2
  BREAST                                                      0
  COLON                                                       0
  LIVER                                                       0
  OTHER EXTRANODAL SITE                                       0
  PAROTID GLAND                                               1
  SMALL INTESTINE                                             1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)               0
  STOMACH                                                     0
  THYROID                                                     0
                                               clus
vv                                              XQ GAIN WILD-TYPE
  ADRENAL                                                       2
  ASCITES/PERITONEUM                                            2
  BONE                                                          4
  BRAIN                                                         1
  BREAST                                                        1
  COLON                                                         2
  LIVER                                                         1
  OTHER EXTRANODAL SITE                                         1
  PAROTID GLAND                                                 0
  SMALL INTESTINE                                               2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                 1
  STOMACH                                                       2
  THYROID                                                       2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V4, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    4  3
  XQ GAIN WILD-TYPE 22 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      4    3
  XQ GAIN WILD-TYPE   22   19
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               4                22
  MALE                 3                19
[1] 2 2
[1] FALSE
D34V5, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    7  0
  XQ GAIN WILD-TYPE 33  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      7    0
  XQ GAIN WILD-TYPE   33    7
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                7                33
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  XQ GAIN MUTATED                                                                                   4
  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
D34V6, multiclass
                                                                                   clus
vv                                                                                  XQ GAIN MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)               4
  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     4
  XQ GAIN WILD-TYPE    15                         1    25
D34V7, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   4                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    4  3
  XQ GAIN WILD-TYPE  8 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      4    3
  XQ GAIN WILD-TYPE    8   33
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 8
  NOT HISPANIC OR LATINO               3                33
[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 35  9
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                44 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                0                 9 
$`1P LOSS MUTATED`
TCGA-FA-A6HO TCGA-G8-6325 TCGA-RQ-A68N 
       24.62        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        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       12.66        31.96        41.16        70.06       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
      116.81       196.60       150.51        98.07        51.98        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV 
       43.86        57.17        32.28        38.24       128.12        24.00 
TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 
       53.16        45.14       109.58        25.15       111.58        12.85 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            24.62              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            51.98            211.23 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           25.910            29.225 
[1] "24.6 - 52.0 (25.9)" "0.0 - 211.2 (29.2)"
[1] "hr="     "7.5e+07"
D35V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  1P LOSS MUTATED         0                  0    0     1      0     0     0
  1P LOSS WILD-TYPE       2                  2    4     2      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  1P LOSS MUTATED                       0             0               0
  1P LOSS WILD-TYPE                     1             1               3
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  1P LOSS MUTATED                                               0       0
  1P LOSS WILD-TYPE                                             1       2
                   vv
clus                THYROID
  1P LOSS MUTATED         0
  1P LOSS WILD-TYPE       2
D35V3, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                24 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A7DS 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FA-A82F        TCGA-FF-8043        TCGA-FF-8061        TCGA-FF-8062 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FF-A7CQ        TCGA-FF-A7CR        TCGA-FF-A7CW        TCGA-FF-A7CX 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FM-8000        TCGA-G8-6324        TCGA-G8-6326        TCGA-G8-6906 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GR-7351        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GS-A9TT        TCGA-RQ-A6JB        TCGA-RQ-AAAT        TCGA-VB-A8QN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D35V4, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1  2
  1P LOSS WILD-TYPE 25 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    2
  1P LOSS WILD-TYPE   25   20
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               1                25
  MALE                 2                20
[1] 2 2
[1] FALSE
D35V5, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    3  0
  1P LOSS WILD-TYPE 37  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    0
  1P LOSS WILD-TYPE   37    7
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                3                37
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  1P LOSS MUTATED                                                                                   2
  1P LOSS WILD-TYPE                                                                                39
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  1P LOSS MUTATED                          1                                  0
  1P LOSS WILD-TYPE                        2                                  4
D35V6, 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)                39
  PRIMARY DLBCL OF THE CNS                                                                          2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       1                         0     2
  1P LOSS WILD-TYPE    17                         1    27
D35V7, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   1                17
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   2                27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1  2
  1P LOSS WILD-TYPE 11 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    2
  1P LOSS WILD-TYPE   11   34
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               2                34
[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 34  9
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                4                43 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                0                 9 
$`3P LOSS MUTATED`
TCGA-FA-A86F TCGA-GS-A9TQ TCGA-GS-A9TZ TCGA-RQ-AAAT 
       18.18        32.28        25.15         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        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
        8.15        14.04        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       12.66        31.96        41.16        51.98        70.06       211.23 
TCGA-G8-6907 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        51.98 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV 
       42.71        43.86        57.17        38.24       128.12        24.00 
TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N 
       53.16        45.14       109.58       111.58        12.85        25.91 
TCGA-RQ-A6JB 
        0.03 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.56              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            32.28            211.23 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           21.665            31.100 
[1] "0.6 - 32.3 (21.7)"  "0.0 - 211.2 (31.1)"
[1] "hr="     "7.4e+07"
D36V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  3P LOSS MUTATED         0                  0    0     1      0     0     0
  3P LOSS WILD-TYPE       2                  2    4     2      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  3P LOSS MUTATED                       0             0               0
  3P LOSS WILD-TYPE                     1             1               3
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  3P LOSS MUTATED                                               0       0
  3P LOSS WILD-TYPE                                             1       2
                   vv
clus                THYROID
  3P LOSS MUTATED         0
  3P LOSS WILD-TYPE       2
D36V3, multiclass
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                24 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A7DS 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FA-A82F        TCGA-FF-8043        TCGA-FF-8061        TCGA-FF-8062 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FF-A7CQ        TCGA-FF-A7CR        TCGA-FF-A7CW        TCGA-FF-A7CX 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FM-8000        TCGA-G8-6324        TCGA-G8-6326        TCGA-G8-6906 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GR-7351        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GS-A9TT        TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-VB-A8QN 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
D36V4, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    3  1
  3P LOSS WILD-TYPE 23 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3    1
  3P LOSS WILD-TYPE   23   21
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               3                23
  MALE                 1                21
[1] 2 2
[1] FALSE
D36V5, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    3  1
  3P LOSS WILD-TYPE 37  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3    1
  3P LOSS WILD-TYPE   37    6
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                3                37
  YES               1                 6
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  3P LOSS MUTATED                                                                                   2
  3P LOSS WILD-TYPE                                                                                39
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  3P LOSS MUTATED                          1                                  1
  3P LOSS WILD-TYPE                        2                                  3
D36V6, multiclass
                                                                                   clus
vv                                                                                  3P 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                                                                                  3P 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
  3P LOSS MUTATED       0                         0     4
  3P LOSS WILD-TYPE    18                         1    25
D36V7, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   0                18
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   4                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    3  1
  3P LOSS WILD-TYPE  9 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3    1
  3P LOSS WILD-TYPE    9   35
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO               1                35
[1] 2 2
[1] FALSE

Clustering(37) Variable = 3Q LOSS MUTATION ANALYSIS
D37V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    3  0
  3Q LOSS WILD-TYPE 35  9
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                44 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                0                 9 
$`3Q LOSS MUTATED`
TCGA-GS-A9TQ TCGA-GS-A9TZ TCGA-RQ-AAAT 
       32.28        25.15         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        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       24.69         4.14        27.35        22.32         9.80        10.29 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       26.01        12.66        31.96        41.16        51.98        70.06 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 
      211.23        19.56       116.81       196.60       150.51        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU 
       51.98        42.71        43.86        57.17        38.24       128.12 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9U3 TCGA-GS-A9U4 
       24.00        53.16        45.14       109.58       111.58        12.85 
TCGA-RQ-A68N TCGA-RQ-A6JB 
       25.91         0.03 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.56              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            32.28            211.23 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           25.150            29.225 
[1] "0.6 - 32.3 (25.1)"  "0.0 - 211.2 (29.2)"
[1] "hr="     "2.6e+07"
D37V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  3Q LOSS MUTATED         0                  0    0     1      0     0     0
  3Q LOSS WILD-TYPE       2                  2    4     2      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  3Q LOSS MUTATED                       0             0               0
  3Q LOSS WILD-TYPE                     1             1               3
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  3Q LOSS MUTATED                                               0       0
  3Q LOSS WILD-TYPE                                             1       2
                   vv
clus                THYROID
  3Q LOSS MUTATED         0
  3Q LOSS WILD-TYPE       2
D37V3, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                24 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A7DS 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FA-A82F        TCGA-FF-8043        TCGA-FF-8061        TCGA-FF-8062 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FF-A7CQ        TCGA-FF-A7CR        TCGA-FF-A7CW        TCGA-FF-A7CX 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FM-8000        TCGA-G8-6324        TCGA-G8-6326        TCGA-G8-6906 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GR-7351        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GS-A9TT        TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-VB-A8QN 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
D37V4, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    2  1
  3Q LOSS WILD-TYPE 24 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    1
  3Q LOSS WILD-TYPE   24   21
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               2                24
  MALE                 1                21
[1] 2 2
[1] FALSE
D37V5, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    2  1
  3Q LOSS WILD-TYPE 38  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    1
  3Q LOSS WILD-TYPE   38    6
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                2                38
  YES               1                 6
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  3Q LOSS MUTATED                                                                                   1
  3Q LOSS WILD-TYPE                                                                                40
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  3Q LOSS MUTATED                          1                                  1
  3Q LOSS WILD-TYPE                        2                                  3
D37V6, multiclass
                                                                                   clus
vv                                                                                  3Q 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                                                                                  3Q LOSS WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                40
  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     3
  3Q LOSS WILD-TYPE    18                         1    26
D37V7, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   0                18
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V8, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    3  0
  3Q LOSS WILD-TYPE  9 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    0
  3Q LOSS WILD-TYPE    9   36
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO               0                36
[1] 2 2
[1] FALSE

Clustering(38) Variable = 4P LOSS MUTATION ANALYSIS
D38V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    3  0
  4P LOSS WILD-TYPE 35  9
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                3                44 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                0                 9 
$`4P LOSS MUTATED`
TCGA-FA-A6HO TCGA-FA-A86F TCGA-GS-A9TQ 
       24.62        18.18        32.28 

$`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        23.64         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        70.06       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
      116.81       196.60       150.51        98.07        51.98        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       43.86        57.17        38.24       128.12        24.00        53.16 
TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N 
       45.14       109.58        25.15       111.58        12.85        25.91 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            18.18              0.03 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            32.28            211.23 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           24.620            29.225 
[1] "18.2 - 32.3 (24.6)" "0.0 - 211.2 (29.2)"
[1] "hr="     "7.4e+07"
D38V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  4P LOSS MUTATED         0                  0    0     0      0     0     0
  4P LOSS WILD-TYPE       2                  2    4     3      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  4P LOSS MUTATED                       0             0               0
  4P LOSS WILD-TYPE                     1             1               3
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  4P LOSS MUTATED                                               0       0
  4P LOSS WILD-TYPE                                             1       2
                   vv
clus                THYROID
  4P LOSS MUTATED         0
  4P LOSS WILD-TYPE       2
D38V3, multiclass
D38V4, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    3  0
  4P LOSS WILD-TYPE 23 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3    0
  4P LOSS WILD-TYPE   23   22
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               3                23
  MALE                 0                22
[1] 2 2
[1] FALSE
D38V5, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    3  0
  4P LOSS WILD-TYPE 37  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3    0
  4P LOSS WILD-TYPE   37    7
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                3                37
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  4P LOSS MUTATED                                                                                   3
  4P LOSS WILD-TYPE                                                                                38
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  4P LOSS MUTATED                          0                                  0
  4P LOSS WILD-TYPE                        3                                  4
D38V6, 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)                38
  PRIMARY DLBCL OF THE CNS                                                                          3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       1                         0     2
  4P LOSS WILD-TYPE    17                         1    27
D38V7, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   1                17
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   2                27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V8, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    1  2
  4P LOSS WILD-TYPE 11 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1    2
  4P LOSS WILD-TYPE   11   34
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               2                34
[1] 2 2
[1] FALSE

Clustering(39) Variable = 4Q LOSS MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    4  0
  4Q LOSS WILD-TYPE 34  9
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4                43 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                0                 9 
$`4Q LOSS MUTATED`
TCGA-FA-A86F TCGA-FF-8043 TCGA-FF-8047 TCGA-GS-A9TQ 
       18.18        31.73         4.14        32.28 

$`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        24.62        23.64 
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        70.06       211.23        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        98.07        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       57.17        38.24       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             4.14              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            32.28            211.23 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           24.955            27.350 
[1] "4.1 - 32.3 (25.0)"  "0.0 - 211.2 (27.4)"
[1] "hr="     "7.4e+07"
D39V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  4Q LOSS MUTATED         0                  0    0     0      0     1     0
  4Q LOSS WILD-TYPE       2                  2    4     3      1     1     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  4Q LOSS MUTATED                       0             0               0
  4Q LOSS WILD-TYPE                     1             1               3
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  4Q LOSS MUTATED                                               0       0
  4Q LOSS WILD-TYPE                                             1       2
                   vv
clus                THYROID
  4Q LOSS MUTATED         0
  4Q LOSS WILD-TYPE       2
D39V3, multiclass
[1] "Remove cluster labels:" "4Q LOSS MUTATED"       
clus
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                1                24 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A7DS 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FA-A82F        TCGA-FF-8061        TCGA-FF-8062        TCGA-FF-A7CQ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FF-A7CR        TCGA-FF-A7CW        TCGA-FF-A7CX        TCGA-FM-8000 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6326        TCGA-G8-6906        TCGA-GR-7351 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D9        TCGA-GS-A9TT 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-RQ-AAAT        TCGA-VB-A8QN 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
D39V4, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    4  0
  4Q LOSS WILD-TYPE 22 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      4    0
  4Q LOSS WILD-TYPE   22   22
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               4                22
  MALE                 0                22
[1] 2 2
[1] FALSE
D39V5, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    4  0
  4Q LOSS WILD-TYPE 36  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      4    0
  4Q LOSS WILD-TYPE   36    7
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                4                36
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  4Q LOSS MUTATED                                                                                   4
  4Q LOSS WILD-TYPE                                                                                37
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  4Q LOSS MUTATED                          0                                  0
  4Q LOSS WILD-TYPE                        3                                  4
D39V6, 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)                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
  4Q LOSS MUTATED       2                         0     2
  4Q LOSS WILD-TYPE    16                         1    27
D39V7, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   2                16
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   2                27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V8, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    1  3
  4Q LOSS WILD-TYPE 11 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1    3
  4Q LOSS WILD-TYPE   11   33
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               3                33
[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 33  7
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7                40 
  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        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       24.69         4.14        27.35        22.32         9.80        10.29 
TCGA-FF-A7CW TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6907 
       26.01        31.96        41.16        51.98        70.06        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
      116.81       196.60       150.51        98.07        51.98        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       57.17        32.28        38.24       128.12        24.00        53.16 
TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-RQ-A6JB 
       45.14        25.15       111.58         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 
           25.910            29.225 
[1] "0.6 - 211.2 (25.9)" "0.0 - 196.6 (29.2)"
[1] "hr=" "1.2"
D40V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  6Q LOSS MUTATED         1                  0    1     2      0     0     0
  6Q LOSS WILD-TYPE       1                  2    3     1      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  6Q LOSS MUTATED                       1             0               0
  6Q LOSS WILD-TYPE                     0             1               3
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  6Q LOSS MUTATED                                               0       0
  6Q LOSS WILD-TYPE                                             1       2
                   vv
clus                THYROID
  6Q LOSS MUTATED         0
  6Q LOSS WILD-TYPE       2
D40V3, multiclass
                                               clus
vv                                              6Q LOSS MUTATED
  ADRENAL                                                     1
  ASCITES/PERITONEUM                                          0
  BONE                                                        1
  BRAIN                                                       2
  BREAST                                                      0
  COLON                                                       0
  LIVER                                                       0
  OTHER EXTRANODAL SITE                                       1
  PAROTID GLAND                                               0
  SMALL INTESTINE                                             0
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)               0
  STOMACH                                                     0
  THYROID                                                     0
                                               clus
vv                                              6Q LOSS WILD-TYPE
  ADRENAL                                                       1
  ASCITES/PERITONEUM                                            2
  BONE                                                          3
  BRAIN                                                         1
  BREAST                                                        1
  COLON                                                         2
  LIVER                                                         1
  OTHER EXTRANODAL SITE                                         0
  PAROTID GLAND                                                 1
  SMALL INTESTINE                                               3
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                 1
  STOMACH                                                       2
  THYROID                                                       2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V4, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    4  3
  6Q LOSS WILD-TYPE 22 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4    3
  6Q LOSS WILD-TYPE   22   19
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               4                22
  MALE                 3                19
[1] 2 2
[1] FALSE
D40V5, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    7  0
  6Q LOSS WILD-TYPE 33  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      7    0
  6Q LOSS WILD-TYPE   33    7
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                7                33
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  6Q LOSS MUTATED                                                                                   5
  6Q LOSS WILD-TYPE                                                                                36
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  6Q LOSS MUTATED                          2                                  0
  6Q LOSS WILD-TYPE                        1                                  4
D40V6, 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)                36
  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    23
D40V7, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   1                17
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   6                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"
D40V8, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    4  3
  6Q LOSS WILD-TYPE  8 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4    3
  6Q LOSS WILD-TYPE    8   33
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 8
  NOT HISPANIC OR LATINO               3                33
[1] 2 2
[1] FALSE

Clustering(41) Variable = 8P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    7  1
  8P LOSS WILD-TYPE 31  8
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                8                39 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                 8 
$`8P LOSS MUTATED`
TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FA-A86F TCGA-FF-8047 TCGA-GR-A4D6 TCGA-GS-A9TY 
       24.62         8.15        18.18         4.14        43.86       109.58 
TCGA-GS-A9TZ TCGA-RQ-A68N 
       25.15        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        23.64        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        70.06       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        51.98        42.71        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9U3 
       38.24       128.12        24.00        53.16        45.14       111.58 
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 
           24.885            31.730 
[1] "4.1 - 109.6 (24.9)" "0.0 - 211.2 (31.7)"
[1] "hr=" "1.1"
D41V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  8P LOSS MUTATED         0                  0    0     1      0     0     0
  8P LOSS WILD-TYPE       2                  2    4     2      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  8P LOSS MUTATED                       0             0               0
  8P LOSS WILD-TYPE                     1             1               3
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  8P LOSS MUTATED                                               0       0
  8P LOSS WILD-TYPE                                             1       2
                   vv
clus                THYROID
  8P LOSS MUTATED         0
  8P LOSS WILD-TYPE       2
D41V3, multiclass
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                24 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A7DS 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FA-A82F        TCGA-FF-8043        TCGA-FF-8061        TCGA-FF-8062 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FF-A7CQ        TCGA-FF-A7CR        TCGA-FF-A7CW        TCGA-FF-A7CX 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FM-8000        TCGA-G8-6324        TCGA-G8-6326        TCGA-G8-6906 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GR-7351        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GS-A9TT        TCGA-RQ-A6JB        TCGA-RQ-AAAT        TCGA-VB-A8QN 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
D41V4, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    6  2
  8P LOSS WILD-TYPE 20 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      6    2
  8P LOSS WILD-TYPE   20   20
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               6                20
  MALE                 2                20
[1] 2 2
[1] FALSE
D41V5, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    7  1
  8P LOSS WILD-TYPE 33  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      7    1
  8P LOSS WILD-TYPE   33    6
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                7                33
  YES               1                 6
[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                                                                                35
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  8P LOSS MUTATED                          1                                  1
  8P LOSS WILD-TYPE                        2                                  3
D41V6, 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)                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
  8P LOSS MUTATED       4                         0     4
  8P LOSS WILD-TYPE    14                         1    25
D41V7, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   4                14
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   4                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    3  5
  8P LOSS WILD-TYPE  9 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3    5
  8P LOSS WILD-TYPE    9   31
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 9
  NOT HISPANIC OR LATINO               5                31
[1] 2 2
[1] FALSE

Clustering(42) Variable = 8Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    4  0
  8Q LOSS WILD-TYPE 34  9
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                43 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                0                 9 
$`8Q LOSS MUTATED`
TCGA-FA-A6HO TCGA-FA-A86F TCGA-GS-A9TY TCGA-RQ-A68N 
       24.62        18.18       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        23.64         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        70.06       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
      116.81       196.60       150.51        98.07        51.98        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV 
       43.86        57.17        32.28        38.24       128.12        24.00 
TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB 
       53.16        45.14        25.15       111.58        12.85         0.03 
TCGA-RQ-AAAT 
        0.56 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            18.18              0.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           109.58            211.23 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           25.265            31.100 
[1] "18.2 - 109.6 (25.3)" "0.0 - 211.2 (31.1)" 
[1] "hr="     "7.7e+07"
D42V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  8Q LOSS MUTATED         0                  0    0     1      0     0     0
  8Q LOSS WILD-TYPE       2                  2    4     2      1     2     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  8Q LOSS MUTATED                       0             0               0
  8Q LOSS WILD-TYPE                     1             1               3
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  8Q LOSS MUTATED                                               0       0
  8Q LOSS WILD-TYPE                                             1       2
                   vv
clus                THYROID
  8Q LOSS MUTATED         0
  8Q LOSS WILD-TYPE       2
D42V3, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                24 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A7DS 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FA-A82F        TCGA-FF-8043        TCGA-FF-8061        TCGA-FF-8062 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FF-A7CQ        TCGA-FF-A7CR        TCGA-FF-A7CW        TCGA-FF-A7CX 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FM-8000        TCGA-G8-6324        TCGA-G8-6326        TCGA-G8-6906 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GR-7351        TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GS-A9TT        TCGA-RQ-A6JB        TCGA-RQ-AAAT        TCGA-VB-A8QN 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D42V4, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    3  1
  8Q LOSS WILD-TYPE 23 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3    1
  8Q LOSS WILD-TYPE   23   21
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               3                23
  MALE                 1                21
[1] 2 2
[1] FALSE
D42V5, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    4  0
  8Q LOSS WILD-TYPE 36  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      4    0
  8Q LOSS WILD-TYPE   36    7
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                4                36
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  8Q LOSS MUTATED                                                                                   3
  8Q LOSS WILD-TYPE                                                                                38
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  8Q LOSS MUTATED                          1                                  0
  8Q LOSS WILD-TYPE                        2                                  4
D42V6, 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)                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
  8Q LOSS MUTATED       1                         0     3
  8Q LOSS WILD-TYPE    17                         1    26
D42V7, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   1                17
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V8, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    2  2
  8Q LOSS WILD-TYPE 10 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    2
  8Q LOSS WILD-TYPE   10   34
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                10
  NOT HISPANIC OR LATINO               2                34
[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 35  9
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 3                 44 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 0                  9 
$`13Q LOSS MUTATED`
TCGA-GR-A4D4 TCGA-GS-A9TZ TCGA-RQ-AAAT 
       51.98        25.15         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        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       24.69         4.14        27.35        22.32         9.80        10.29 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       26.01        12.66        31.96        41.16        51.98        70.06 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 
      211.23        19.56       116.81       196.60       150.51        98.07 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU 
       42.71        43.86        57.17        32.28        38.24       128.12 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9U3 TCGA-GS-A9U4 
       24.00        53.16        45.14       109.58       111.58        12.85 
TCGA-RQ-A68N TCGA-RQ-A6JB 
       25.91         0.03 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.56               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             51.98             211.23 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            25.150             29.225 
[1] "0.6 - 52.0 (25.1)"  "0.0 - 211.2 (29.2)"
[1] "hr="     "7.2e+07"
D43V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  13Q LOSS MUTATED         0                  0    1     1      0     0     0
  13Q LOSS WILD-TYPE       2                  2    3     2      1     2     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  13Q LOSS MUTATED                       0             0               0
  13Q LOSS WILD-TYPE                     1             1               3
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  13Q LOSS MUTATED                                               0       0
  13Q LOSS WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  13Q LOSS MUTATED         0
  13Q LOSS WILD-TYPE       2
D43V3, multiclass
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                 23 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FA-A7DS         TCGA-FA-A82F         TCGA-FF-8043 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FF-8061         TCGA-FF-8062         TCGA-FF-A7CQ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FF-A7CR         TCGA-FF-A7CW         TCGA-FF-A7CX 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6326 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G8-6906         TCGA-GR-7351         TCGA-GR-A4D5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GR-A4D9         TCGA-GS-A9TT         TCGA-RQ-A68N 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-RQ-A6JB         TCGA-VB-A8QN 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D43V4, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    2  1
  13Q LOSS WILD-TYPE 24 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2    1
  13Q LOSS WILD-TYPE   24   21
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                2                 24
  MALE                  1                 21
[1] 2 2
[1] FALSE
D43V5, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    2  1
  13Q LOSS WILD-TYPE 38  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2    1
  13Q LOSS WILD-TYPE   38    6
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 2                 38
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  13Q LOSS MUTATED                                                                                   1
  13Q LOSS WILD-TYPE                                                                                40
                    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
D43V6, 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)                 40
  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    26
D43V7, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    0                 18
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                 26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V8, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    2  1
  13Q LOSS WILD-TYPE 10 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2    1
  13Q LOSS WILD-TYPE   10   35
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                1                 35
[1] 2 2
[1] FALSE

Clustering(44) Variable = 15Q LOSS MUTATION ANALYSIS
D44V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    7  0
  15Q LOSS WILD-TYPE 31  9
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                 40 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 0                  9 
$`15Q LOSS MUTATED`
TCGA-FA-A6HO TCGA-FA-A86F TCGA-FF-8043 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
       24.62        18.18        31.73        98.07        51.98        43.86 
TCGA-GS-A9TQ 
       32.28 

$`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        23.64         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        70.06       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       128.12 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 
       24.00        53.16        45.14       109.58        25.15       111.58 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85        25.91         0.03         0.56 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             18.18               0.03 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             98.07             211.23 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             32.28              25.96 
[1] "18.2 - 98.1 (32.3)" "0.0 - 211.2 (26.0)"
[1] "hr="     "2.4e+08"
D44V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  15Q LOSS MUTATED         0                  0    1     0      0     1     0
  15Q LOSS WILD-TYPE       2                  2    3     3      1     1     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  15Q LOSS MUTATED                       0             0               0
  15Q LOSS WILD-TYPE                     1             1               3
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  15Q LOSS MUTATED                                               0       0
  15Q LOSS WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  15Q LOSS MUTATED         0
  15Q LOSS WILD-TYPE       2
D44V3, multiclass
[1] "Remove cluster labels:" "15Q LOSS MUTATED"      
clus
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 2                 23 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FA-A7DS         TCGA-FA-A82F         TCGA-FF-8061 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FF-8062         TCGA-FF-A7CQ         TCGA-FF-A7CR 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FF-A7CW         TCGA-FF-A7CX         TCGA-FM-8000 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G8-6324         TCGA-G8-6326         TCGA-G8-6906 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-A4D5         TCGA-GR-A4D9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GS-A9TT         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-RQ-AAAT         TCGA-VB-A8QN 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
D44V4, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    6  1
  15Q LOSS WILD-TYPE 20 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      6    1
  15Q LOSS WILD-TYPE   20   21
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                6                 20
  MALE                  1                 21
[1] 2 2
[1] FALSE
D44V5, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    7  0
  15Q LOSS WILD-TYPE 33  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7    0
  15Q LOSS WILD-TYPE   33    7
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 7                 33
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  15Q LOSS MUTATED                                                                                   7
  15Q LOSS WILD-TYPE                                                                                34
                    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
D44V6, 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)                 34
  PRIMARY DLBCL OF THE CNS                                                                           3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       3                         0     4
  15Q LOSS WILD-TYPE    15                         1    25
D44V7, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    4                 25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V8, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    1  6
  15Q LOSS WILD-TYPE 11 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    6
  15Q LOSS WILD-TYPE   11   30
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 11
  NOT HISPANIC OR LATINO                6                 30
[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 34  9
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 43 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 0                  9 
$`16Q LOSS MUTATED`
TCGA-FA-A6HO TCGA-FF-8043 TCGA-FF-8047 TCGA-GR-A4D4 
       24.62        31.73         4.14        51.98 

$`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        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8061 
       14.04        18.18        35.54        31.10        24.69        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-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        70.06       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-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       32.28        38.24       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              4.14               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             51.98             211.23 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            28.175             27.350 
[1] "4.1 - 52.0 (28.2)"  "0.0 - 211.2 (27.4)"
[1] "hr="     "7.5e+07"
D45V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  16Q LOSS MUTATED         0                  0    1     0      0     1     0
  16Q LOSS WILD-TYPE       2                  2    3     3      1     1     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  16Q LOSS MUTATED                       0             0               0
  16Q LOSS WILD-TYPE                     1             1               3
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  16Q LOSS MUTATED                                               0       0
  16Q LOSS WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  16Q LOSS MUTATED         0
  16Q LOSS WILD-TYPE       2
D45V3, multiclass
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 23 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FA-A7DS         TCGA-FA-A82F         TCGA-FF-8061 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FF-8062         TCGA-FF-A7CQ         TCGA-FF-A7CR 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FF-A7CW         TCGA-FF-A7CX         TCGA-FM-8000 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G8-6324         TCGA-G8-6326         TCGA-G8-6906 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-A4D5         TCGA-GR-A4D9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GS-A9TT         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-RQ-AAAT         TCGA-VB-A8QN 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D45V4, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    4  0
  16Q LOSS WILD-TYPE 22 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4    0
  16Q LOSS WILD-TYPE   22   22
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                4                 22
  MALE                  0                 22
[1] 2 2
[1] FALSE
D45V5, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    4  0
  16Q LOSS WILD-TYPE 36  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4    0
  16Q LOSS WILD-TYPE   36    7
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 4                 36
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  16Q LOSS MUTATED                                                                                   4
  16Q LOSS WILD-TYPE                                                                                37
                    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
D45V6, 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)                 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
  16Q LOSS MUTATED       3                         0     1
  16Q LOSS WILD-TYPE    15                         1    28
D45V7, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    1                 28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V8, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    0  4
  16Q LOSS WILD-TYPE 12 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      0    4
  16Q LOSS WILD-TYPE   12   32
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                4                 32
[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 29  9
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 9                 38 
  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 
       24.62        14.04        51.98        32.28        53.16       109.58 
TCGA-GS-A9TZ TCGA-RQ-A68N TCGA-RQ-AAAT 
       25.15        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        23.64         8.15 
TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
       18.18        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       31.96        41.16        51.98        70.06       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 
      116.81       196.60       150.51        98.07        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9U3 
       57.17        38.24       128.12        24.00        45.14       111.58 
TCGA-GS-A9U4 TCGA-RQ-A6JB 
       12.85         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 
            25.910             29.225 
[1] "0.6 - 109.6 (25.9)" "0.0 - 211.2 (29.2)"
[1] "hr="     "2.6e+08"
D46V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  17P LOSS MUTATED         0                  0    1     2      0     0     0
  17P LOSS WILD-TYPE       2                  2    3     1      1     2     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  17P LOSS MUTATED                       0             0               1
  17P LOSS WILD-TYPE                     1             1               2
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  17P LOSS MUTATED                                               0       0
  17P LOSS WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  17P LOSS MUTATED         0
  17P LOSS WILD-TYPE       2
D46V3, multiclass
                                               clus
vv                                              17P LOSS MUTATED
  ADRENAL                                                      0
  ASCITES/PERITONEUM                                           0
  BONE                                                         1
  BRAIN                                                        2
  BREAST                                                       0
  COLON                                                        0
  LIVER                                                        0
  OTHER EXTRANODAL SITE                                        0
  PAROTID GLAND                                                0
  SMALL INTESTINE                                              1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                0
  STOMACH                                                      0
  THYROID                                                      0
                                               clus
vv                                              17P LOSS WILD-TYPE
  ADRENAL                                                        2
  ASCITES/PERITONEUM                                             2
  BONE                                                           3
  BRAIN                                                          1
  BREAST                                                         1
  COLON                                                          2
  LIVER                                                          1
  OTHER EXTRANODAL SITE                                          1
  PAROTID GLAND                                                  1
  SMALL INTESTINE                                                2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                  1
  STOMACH                                                        2
  THYROID                                                        2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V4, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    7  2
  17P LOSS WILD-TYPE 19 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      7    2
  17P LOSS WILD-TYPE   19   20
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                7                 19
  MALE                  2                 20
[1] 2 2
[1] FALSE
D46V5, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    7  2
  17P LOSS WILD-TYPE 33  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      7    2
  17P LOSS WILD-TYPE   33    5
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 7                 33
  YES                2                  5
[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                                                                                36
                    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
D46V6, 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)                 36
  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    22
D46V7, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    2                 16
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    7                 22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    6  3
  17P LOSS WILD-TYPE  6 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      6    3
  17P LOSS WILD-TYPE    6   33
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  6
  NOT HISPANIC OR LATINO                3                 33
[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 34  9
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                 43 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 0                  9 
$`17Q LOSS MUTATED`
TCGA-GS-A9TQ TCGA-GS-A9TZ TCGA-RQ-A68N TCGA-RQ-AAAT 
       32.28        25.15        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        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        8.15        14.04        18.18        35.54        31.10        31.73 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       24.69         4.14        27.35        22.32         9.80        10.29 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       26.01        12.66        31.96        41.16        51.98        70.06 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 
      211.23        19.56       116.81       196.60       150.51        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU 
       51.98        42.71        43.86        57.17        38.24       128.12 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9U3 TCGA-GS-A9U4 
       24.00        53.16        45.14       109.58       111.58        12.85 
TCGA-RQ-A6JB 
        0.03 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.56               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             32.28             211.23 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             25.53              31.10 
[1] "0.6 - 32.3 (25.5)"  "0.0 - 211.2 (31.1)"
[1] "hr="     "7.5e+07"
D47V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  17Q LOSS MUTATED         0                  0    0     2      0     0     0
  17Q LOSS WILD-TYPE       2                  2    4     1      1     2     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  17Q LOSS MUTATED                       0             0               0
  17Q LOSS WILD-TYPE                     1             1               3
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  17Q LOSS MUTATED                                               0       0
  17Q LOSS WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  17Q LOSS MUTATED         0
  17Q LOSS WILD-TYPE       2
D47V3, multiclass
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 23 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FA-A7DS         TCGA-FA-A82F         TCGA-FF-8043 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FF-8061         TCGA-FF-8062         TCGA-FF-A7CQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FF-A7CR         TCGA-FF-A7CW         TCGA-FF-A7CX 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FM-8000         TCGA-G8-6324         TCGA-G8-6326 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G8-6906         TCGA-GR-7351         TCGA-GR-A4D4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GR-A4D5         TCGA-GR-A4D9         TCGA-GS-A9TT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-RQ-A6JB         TCGA-VB-A8QN 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
D47V4, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    2  2
  17Q LOSS WILD-TYPE 24 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    2
  17Q LOSS WILD-TYPE   24   20
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                2                 24
  MALE                  2                 20
[1] 2 2
[1] FALSE
D47V5, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    3  1
  17Q LOSS WILD-TYPE 37  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3    1
  17Q LOSS WILD-TYPE   37    6
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 3                 37
  YES                1                  6
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  17Q LOSS MUTATED                                                                                   1
  17Q LOSS WILD-TYPE                                                                                40
                    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
D47V6, 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)                 40
  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    25
D47V7, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                 18
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    4                 25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V8, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    4  0
  17Q LOSS WILD-TYPE  8 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    0
  17Q LOSS WILD-TYPE    8   36
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  8
  NOT HISPANIC OR LATINO                0                 36
[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 34  8
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                 42 
  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        32.28         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        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       31.96        41.16        70.06       211.23        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        98.07        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       57.17        38.24       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 

  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 
            23.280             29.225 
[1] "0.6 - 52.0 (23.3)"  "0.0 - 211.2 (29.2)"
[1] "hr=" "1.7"
D48V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  18P LOSS MUTATED         1                  0    0     1      0     0     0
  18P LOSS WILD-TYPE       1                  2    4     2      1     2     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  18P LOSS MUTATED                       0             0               1
  18P LOSS WILD-TYPE                     1             1               2
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  18P LOSS MUTATED                                               0       0
  18P LOSS WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  18P LOSS MUTATED         0
  18P LOSS WILD-TYPE       2
D48V3, multiclass
                                               clus
vv                                              18P LOSS MUTATED
  ADRENAL                                                      1
  ASCITES/PERITONEUM                                           0
  BONE                                                         0
  BRAIN                                                        1
  BREAST                                                       0
  COLON                                                        0
  LIVER                                                        0
  OTHER EXTRANODAL SITE                                        0
  PAROTID GLAND                                                0
  SMALL INTESTINE                                              1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                0
  STOMACH                                                      0
  THYROID                                                      0
                                               clus
vv                                              18P LOSS WILD-TYPE
  ADRENAL                                                        1
  ASCITES/PERITONEUM                                             2
  BONE                                                           4
  BRAIN                                                          2
  BREAST                                                         1
  COLON                                                          2
  LIVER                                                          1
  OTHER EXTRANODAL SITE                                          1
  PAROTID GLAND                                                  1
  SMALL INTESTINE                                                2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)                  1
  STOMACH                                                        2
  THYROID                                                        2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V4, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    2  3
  18P LOSS WILD-TYPE 24 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    3
  18P LOSS WILD-TYPE   24   19
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                2                 24
  MALE                  3                 19
[1] 2 2
[1] FALSE
D48V5, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    5  0
  18P LOSS WILD-TYPE 35  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      5    0
  18P LOSS WILD-TYPE   35    7
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 5                 35
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  18P LOSS MUTATED                                                                                   4
  18P LOSS WILD-TYPE                                                                                37
                    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
D48V6, 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)                 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
  18P LOSS MUTATED       2                         0     3
  18P LOSS WILD-TYPE    16                         1    26
D48V7, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    2                 16
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                 26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V8, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    2  3
  18P LOSS WILD-TYPE 10 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    3
  18P LOSS WILD-TYPE   10   33
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 10
  NOT HISPANIC OR LATINO                3                 33
[1] 2 2
[1] FALSE

Clustering(49) Variable = 18Q LOSS MUTATION ANALYSIS
D49V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    4  1
  18Q LOSS WILD-TYPE 34  8
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 5                 42 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 1                  8 
$`18Q LOSS MUTATED`
TCGA-FA-A4XK TCGA-G8-6325 TCGA-GS-A9TQ TCGA-GS-A9TY TCGA-RQ-AAAT 
       23.28        51.98        32.28       109.58         0.56 

$`18Q 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        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       12.66        31.96        41.16        70.06       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
      116.81       196.60       150.51        98.07        51.98        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       43.86        57.17        38.24       128.12        24.00        53.16 
TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
       45.14        25.15       111.58        12.85        25.91         0.03 

  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 
             32.28              26.68 
[1] "0.6 - 109.6 (32.3)" "0.0 - 211.2 (26.7)"
[1] "hr=" "1.4"
D49V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  18Q LOSS MUTATED         0                  0    0     1      0     0     0
  18Q LOSS WILD-TYPE       2                  2    4     2      1     2     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  18Q LOSS MUTATED                       0             0               1
  18Q LOSS WILD-TYPE                     1             1               2
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  18Q LOSS MUTATED                                               0       0
  18Q LOSS WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  18Q LOSS MUTATED         0
  18Q LOSS WILD-TYPE       2
D49V3, multiclass
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                 23 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A7DS 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FA-A82F         TCGA-FF-8043         TCGA-FF-8061 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FF-8062         TCGA-FF-A7CQ         TCGA-FF-A7CR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FF-A7CW         TCGA-FF-A7CX         TCGA-FM-8000 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G8-6324         TCGA-G8-6326         TCGA-G8-6906 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GR-7351         TCGA-GR-A4D4         TCGA-GR-A4D5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GR-A4D9         TCGA-GS-A9TT         TCGA-RQ-A68N 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-RQ-A6JB         TCGA-VB-A8QN 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
D49V4, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    3  2
  18Q LOSS WILD-TYPE 23 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3    2
  18Q LOSS WILD-TYPE   23   20
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                3                 23
  MALE                  2                 20
[1] 2 2
[1] FALSE
D49V5, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    5  0
  18Q LOSS WILD-TYPE 35  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      5    0
  18Q LOSS WILD-TYPE   35    7
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 5                 35
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  18Q LOSS MUTATED                                                                                   4
  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
D49V6, multiclass
                                                                                   clus
vv                                                                                  18Q 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                                                                                  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       1                         0     4
  18Q LOSS WILD-TYPE    17                         1    25
D49V7, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    1                 17
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    4                 25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V8, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    3  2
  18Q LOSS WILD-TYPE  9 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3    2
  18Q LOSS WILD-TYPE    9   34
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  9
  NOT HISPANIC OR LATINO                2                 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 35  9
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                 44 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 0                  9 
$`22Q LOSS MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8043 
       24.62        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        23.64         8.15 
TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       18.18        35.54        31.10        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66        31.96 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        70.06       211.23        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        98.07        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       57.17        32.28        38.24       128.12        24.00        53.16 
TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N 
       45.14       109.58        25.15       111.58        12.85        25.91 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             14.04               0.03 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             31.73             211.23 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            24.620             29.225 
[1] "14.0 - 31.7 (24.6)" "0.0 - 211.2 (29.2)"
[1] "hr="     "7.4e+07"
D50V2, continuous
                    vv
clus                 ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  22Q LOSS MUTATED         0                  0    0     0      0     1     0
  22Q LOSS WILD-TYPE       2                  2    4     3      1     1     1
                    vv
clus                 OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  22Q LOSS MUTATED                       0             0               1
  22Q LOSS WILD-TYPE                     1             1               2
                    vv
clus                 SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  22Q LOSS MUTATED                                               0       0
  22Q LOSS WILD-TYPE                                             1       2
                    vv
clus                 THYROID
  22Q LOSS MUTATED         0
  22Q LOSS WILD-TYPE       2
D50V3, multiclass
[1] "Remove cluster labels:" "22Q LOSS MUTATED"      
clus
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 2                 23 
        TCGA-FA-8693         TCGA-FA-A4BB         TCGA-FA-A4XK 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FA-A7DS         TCGA-FF-8061         TCGA-FF-8062 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FF-A7CQ         TCGA-FF-A7CR         TCGA-FF-A7CW 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FF-A7CX         TCGA-FM-8000         TCGA-G8-6324 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G8-6326         TCGA-G8-6906         TCGA-GR-7351 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GR-A4D4         TCGA-GR-A4D5         TCGA-GR-A4D9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GS-A9TT         TCGA-RQ-A68N         TCGA-RQ-A6JB 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-RQ-AAAT         TCGA-VB-A8QN 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
D50V4, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    3  0
  22Q LOSS WILD-TYPE 23 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3    0
  22Q LOSS WILD-TYPE   23   22
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                3                 23
  MALE                  0                 22
[1] 2 2
[1] FALSE
D50V5, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    3  0
  22Q LOSS WILD-TYPE 37  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3    0
  22Q LOSS WILD-TYPE   37    7
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 3                 37
  YES                0                  7
[1] 2 2
[1] FALSE
                    vv
clus                 DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  22Q LOSS MUTATED                                                                                   3
  22Q LOSS WILD-TYPE                                                                                38
                    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
D50V6, 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)                 38
  PRIMARY DLBCL OF THE CNS                                                                           3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       3                         0     0
  22Q LOSS WILD-TYPE    15                         1    29
D50V7, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    3                 15
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    0                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V8, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    0  3
  22Q LOSS WILD-TYPE 12 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      0    3
  22Q LOSS WILD-TYPE   12   33
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 12
  NOT HISPANIC OR LATINO                3                 33
[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 35  7
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                5                42 
  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       111.58 

$`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        24.62        23.64 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8061 
       14.04        18.18        35.54        31.10        24.69        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-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-G8-6909 TCGA-G8-6914 
       41.16        51.98        70.06       211.23       116.81       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      150.51        98.07        51.98        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       32.28        38.24       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
      109.58        25.15        12.85        25.91         0.03         0.56 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             4.14              0.03 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           111.58            211.23 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           19.560            29.225 
[1] "4.1 - 111.6 (19.6)" "0.0 - 211.2 (29.2)"
[1] "hr=" "4.5"
D51V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  XP LOSS MUTATED         0                  0    0     0      0     1     0
  XP LOSS WILD-TYPE       2                  2    4     3      1     1     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  XP LOSS MUTATED                       0             0               0
  XP LOSS WILD-TYPE                     1             1               3
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  XP LOSS MUTATED                                               0       0
  XP LOSS WILD-TYPE                                             1       2
                   vv
clus                THYROID
  XP LOSS MUTATED         0
  XP LOSS WILD-TYPE       2
D51V3, multiclass
[1] "Remove cluster labels:" "XP LOSS MUTATED"       
clus
  XP LOSS MUTATED XP LOSS WILD-TYPE 
                1                24 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A7DS 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FA-A82F        TCGA-FF-8061        TCGA-FF-8062        TCGA-FF-A7CQ 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-FF-A7CR        TCGA-FF-A7CW        TCGA-FF-A7CX        TCGA-FM-8000 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6326        TCGA-G8-6906        TCGA-GR-7351 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D9        TCGA-GS-A9TT 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-RQ-AAAT        TCGA-VB-A8QN 
"XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" "XP LOSS WILD-TYPE" 
D51V4, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    5  0
  XP LOSS WILD-TYPE 21 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      5    0
  XP LOSS WILD-TYPE   21   22
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE               5                21
  MALE                 0                22
[1] 2 2
[1] FALSE
D51V5, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    5  0
  XP LOSS WILD-TYPE 35  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      5    0
  XP LOSS WILD-TYPE   35    7
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO                5                35
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  XP LOSS MUTATED                                                                                   5
  XP LOSS WILD-TYPE                                                                                36
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  XP LOSS MUTATED                          0                                  0
  XP LOSS WILD-TYPE                        3                                  4
D51V6, 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)                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
  XP LOSS MUTATED       3                         0     2
  XP LOSS WILD-TYPE    15                         1    27
D51V7, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   2                27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V8, binary
                   cls
clus                 0  1
  XP LOSS MUTATED    1  4
  XP LOSS WILD-TYPE 11 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      1    4
  XP LOSS WILD-TYPE   11   32
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                11
  NOT HISPANIC OR LATINO               4                32
[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 36  7
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                43 
  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        24.62        23.64 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8061 
       14.04        18.18        35.54        31.10        24.69        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-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-G8-6909 TCGA-G8-6914 
       41.16        51.98        70.06       211.23       116.81       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      150.51        98.07        51.98        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX 
       32.28        38.24       128.12        24.00        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  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            31.100 
[1] "4.1 - 31.7 (13.9)"  "0.0 - 211.2 (31.1)"
[1] "hr=" "8.1"
D52V2, continuous
                   vv
clus                ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  XQ LOSS MUTATED         0                  0    0     0      0     1     0
  XQ LOSS WILD-TYPE       2                  2    4     3      1     1     1
                   vv
clus                OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  XQ LOSS MUTATED                       0             0               0
  XQ LOSS WILD-TYPE                     1             1               3
                   vv
clus                SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH
  XQ LOSS MUTATED                                               0       0
  XQ LOSS WILD-TYPE                                             1       2
                   vv
clus                THYROID
  XQ LOSS MUTATED         0
  XQ LOSS WILD-TYPE       2
D52V3, multiclass
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                24 
       TCGA-FA-8693        TCGA-FA-A4BB        TCGA-FA-A4XK        TCGA-FA-A7DS 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FA-A82F        TCGA-FF-8061        TCGA-FF-8062        TCGA-FF-A7CQ 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FF-A7CR        TCGA-FF-A7CW        TCGA-FF-A7CX        TCGA-FM-8000 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G8-6324        TCGA-G8-6326        TCGA-G8-6906        TCGA-GR-7351 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GR-A4D4        TCGA-GR-A4D5        TCGA-GR-A4D9        TCGA-GS-A9TT 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-RQ-A68N        TCGA-RQ-A6JB        TCGA-RQ-AAAT        TCGA-VB-A8QN 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D52V4, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    4  0
  XQ LOSS WILD-TYPE 22 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4    0
  XQ LOSS WILD-TYPE   22   22
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               4                22
  MALE                 0                22
[1] 2 2
[1] FALSE
D52V5, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    4  0
  XQ LOSS WILD-TYPE 36  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4    0
  XQ LOSS WILD-TYPE   36    7
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                4                36
  YES               0                 7
[1] 2 2
[1] FALSE
                   vv
clus                DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  XQ LOSS MUTATED                                                                                   4
  XQ LOSS WILD-TYPE                                                                                37
                   vv
clus                PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  XQ LOSS MUTATED                          0                                  0
  XQ LOSS WILD-TYPE                        3                                  4
D52V6, 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)                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
  XQ LOSS MUTATED       3                         0     1
  XQ LOSS WILD-TYPE    15                         1    28
D52V7, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   3                15
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   1                28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V8, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    0  4
  XQ LOSS WILD-TYPE 12 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0    4
  XQ LOSS WILD-TYPE   12   32
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                12
  NOT HISPANIC OR LATINO               4                32
[1] 2 2
[1] FALSE
