[1] "ofn"        "-oTDLBC-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/DLBC-TP/19775131/DLBC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/19780778/transformed.cor.cli.txt"

nPatients in clinical file=47, in cluster file=48, common to both=47
[1] "Reduce the number of clustering variables from 41 to 40."
[1] 40 47
[1] "AMP PEAK  1(1Q24.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE 
                           15                            32 
  AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE 
                           15                            32 
[1] "AMP PEAK  2(2P16.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                           15                            32 
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                           15                            32 
[1] "AMP PEAK  3(3Q27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                           14                            33 
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                           14                            33 
[1] "AMP PEAK  4(3Q29) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE 
                         15                          32 
  AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE 
                         15                          32 
[1] "AMP PEAK  5(5P13.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE 
                            8                            39 
  AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE 
                            8                            39 
[1] "AMP PEAK  6(7P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE 
                           16                            31 
  AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE 
                           16                            31 
[1] "AMP PEAK  7(7Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE 
                           15                            32 
  AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE 
                           15                            32 
[1] "AMP PEAK  8(8Q24.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE 
                            14                             33 
  AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE 
                            14                             33 
[1] "AMP PEAK  9(12Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE 
                            14                             33 
  AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE 
                            14                             33 
[1] "AMP PEAK 11(16P12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE 
                            10                             37 
  AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE 
                            10                             37 
[1] "AMP PEAK 12(18Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE 
                            16                             31 
  AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE 
                            16                             31 
[1] "AMP PEAK 13(19Q13.43) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE 
                             10                              37 
  AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE 
                             10                              37 
[1] "AMP PEAK 14(XQ27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE 
                            7                            40 
  AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE 
                            7                            40 
[1] "DEL PEAK  1(1P36.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            11                             36 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            11                             36 
[1] "DEL PEAK  2(1P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                           11                            36 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                           11                            36 
[1] "DEL PEAK  3(1Q43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         10                          37 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         10                          37 
[1] "DEL PEAK  4(2Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                            8                            39 
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                            8                            39 
[1] "DEL PEAK  5(3P21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                             8                             39 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                             8                             39 
[1] "DEL PEAK  6(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE 
                           10                            37 
  DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE 
                           10                            37 
[1] "DEL PEAK  7(5Q33.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(5Q33.3) MUTATED DEL PEAK  7(5Q33.3) WILD-TYPE 
                            4                            43 
  DEL PEAK  7(5Q33.3) MUTATED DEL PEAK  7(5Q33.3) WILD-TYPE 
                            4                            43 
[1] "DEL PEAK  8(6P21.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE 
                             6                             41 
  DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE 
                             6                             41 
[1] "DEL PEAK  9(6Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE 
                           17                            30 
  DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE 
                           17                            30 
[1] "DEL PEAK 10(6Q22.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE 
                            15                             32 
  DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE 
                            15                             32 
[1] "DEL PEAK 11(6Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE 
                           15                            32 
  DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE 
                           15                            32 
[1] "DEL PEAK 12(7Q33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(7Q33) MUTATED DEL PEAK 12(7Q33) WILD-TYPE 
                          5                          42 
  DEL PEAK 12(7Q33) MUTATED DEL PEAK 12(7Q33) WILD-TYPE 
                          5                          42 
[1] "DEL PEAK 13(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                           11                            36 
  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                           11                            36 
[1] "DEL PEAK 14(8Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE 
                            9                            38 
  DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE 
                            9                            38 
[1] "DEL PEAK 15(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                           17                            30 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                           17                            30 
[1] "DEL PEAK 16(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                              8                              39 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                              8                              39 
[1] "DEL PEAK 17(12P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE 
                             8                             39 
  DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE 
                             8                             39 
[1] "DEL PEAK 18(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                             6                             41 
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                             6                             41 
[1] "DEL PEAK 19(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                            13                             34 
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                            13                             34 
[1] "DEL PEAK 20(16P13.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE 
                              5                              42 
  DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE 
                              5                              42 
[1] "DEL PEAK 21(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                             5                             42 
  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                             5                             42 
[1] "DEL PEAK 22(17P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE 
                            12                             35 
  DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE 
                            12                             35 
[1] "DEL PEAK 23(17Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE 
                             7                             40 
  DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE 
                             7                             40 
[1] "DEL PEAK 24(19P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE 
                             4                             43 
  DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE 
                             4                             43 
[1] "DEL PEAK 25(19Q13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE 
                             5                             42 
  DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE 
                             5                             42 
[1] "DEL PEAK 26(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE 
                              7                              40 
  DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE 
                              7                              40 
[1] "DEL PEAK 27(XQ28) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(XQ28) MUTATED DEL PEAK 27(XQ28) WILD-TYPE 
                          3                          44 
  DEL PEAK 27(XQ28) MUTATED DEL PEAK 27(XQ28) WILD-TYPE 
                          3                          44 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "PATHOLOGIC_STAGE"                    
 [6] "PATHOLOGY_T_STAGE"                   
 [7] "PATHOLOGY_N_STAGE"                   
 [8] "PATHOLOGY_M_STAGE"                   
 [9] "GENDER"                              
[10] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[11] "RADIATION_THERAPY"                   
[12] "HISTOLOGICAL_TYPE"                   
[13] "RACE"                                
[14] "ETHNICITY"                           

Input Data has 14 rows and 47 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=40,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PATHOLOGIC_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 47 columns, 1 survival variables, and 6 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"    "GENDER"            "RADIATION_THERAPY"
[4] "HISTOLOGICAL_TYPE" "RACE"              "ETHNICITY"        
YEARS_TO_BIRTH, nv=33, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1Q24.2) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  1(1Q24.2) MUTATED   14  1
  AMP PEAK  1(1Q24.2) WILD-TYPE 24  8
  AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE 
                           15                            32 
  AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE 
                            1                             8 
$`AMP PEAK  1(1Q24.2) MUTATED`
TCGA-FA-A4BB TCGA-FA-A7Q1 TCGA-FA-A86F TCGA-FF-8047 TCGA-FF-A7CW TCGA-FM-8000 
        4.34         8.15        18.18         4.14        26.01        31.96 
TCGA-G8-6325 TCGA-G8-6914 TCGA-GR-7353 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       51.98       196.60        98.07        43.86        57.17        32.28 
TCGA-GS-A9TY TCGA-GS-A9U3 TCGA-RQ-AAAT 
      109.58       111.58         0.56 

$`AMP PEAK  1(1Q24.2) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A82F 
        4.34        23.28         1.91        24.62        23.64        14.04 
TCGA-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-A7CX TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 
        9.80        10.29        12.66        41.16        70.06       211.23 
TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GS-A9TT 
       19.56       116.81       150.51        51.98        42.71        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U4 
      128.12        24.00        53.16        45.14        25.15        12.85 
TCGA-RQ-A68N TCGA-RQ-A6JB 
       25.91         0.03 

  AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE 
                         0.56                          0.03 
  AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE 
                       196.60                        211.23 
  AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE 
                        32.28                         25.53 
[1] "0.6 - 196.6 (32.3)" "0.0 - 211.2 (25.5)"
[1] "hr=" "3"  
D1V2, continuous
D1V3, binary
                               cls
clus                             0  1
  AMP PEAK  1(1Q24.2) MUTATED   10  5
  AMP PEAK  1(1Q24.2) WILD-TYPE 16 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q24.2) MUTATED     10    5
  AMP PEAK  1(1Q24.2) WILD-TYPE   16   16
        clus
vv       AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE
  FEMALE                          10                            16
  MALE                             5                            16
[1] 2 2
[1] FALSE
D1V4, binary
                               cls
clus                             0  1
  AMP PEAK  1(1Q24.2) MUTATED   15  0
  AMP PEAK  1(1Q24.2) WILD-TYPE 24  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q24.2) MUTATED     15    0
  AMP PEAK  1(1Q24.2) WILD-TYPE   24    7
     clus
vv    AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE
  NO                           15                            24
  YES                           0                             7
[1] 2 2
[1] FALSE
                               vv
clus                            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  AMP PEAK  1(1Q24.2) MUTATED                                                                                  14
  AMP PEAK  1(1Q24.2) WILD-TYPE                                                                                26
                               vv
clus                            PRIMARY DLBCL OF THE CNS
  AMP PEAK  1(1Q24.2) MUTATED                          1
  AMP PEAK  1(1Q24.2) WILD-TYPE                        2
                               vv
clus                            PRIMARY MEDIASTINAL (THYMIC) DLBCL
  AMP PEAK  1(1Q24.2) MUTATED                                    0
  AMP PEAK  1(1Q24.2) WILD-TYPE                                  4
D1V5, multiclass
                                                                                   clus
vv                                                                                  AMP PEAK  1(1Q24.2) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                          14
  PRIMARY DLBCL OF THE CNS                                                                                    1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                          0
                                                                                   clus
vv                                                                                  AMP PEAK  1(1Q24.2) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                            26
  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
  AMP PEAK  1(1Q24.2) MUTATED       4                         0    11
  AMP PEAK  1(1Q24.2) WILD-TYPE    14                         1    17
D1V6, multiclass
                           clus
vv                          AMP PEAK  1(1Q24.2) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              11
                           clus
vv                          AMP PEAK  1(1Q24.2) WILD-TYPE
  ASIAN                                                14
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                               cls
clus                             0  1
  AMP PEAK  1(1Q24.2) MUTATED    4 11
  AMP PEAK  1(1Q24.2) WILD-TYPE  8 24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q24.2) MUTATED      4   11
  AMP PEAK  1(1Q24.2) WILD-TYPE    8   24
                        clus
vv                       AMP PEAK  1(1Q24.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          11
                        clus
vv                       AMP PEAK  1(1Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                            24
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(2P16.1) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(2P16.1) MUTATED   11  4
  AMP PEAK  2(2P16.1) WILD-TYPE 27  5
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                           15                            32 
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                            4                             5 
$`AMP PEAK  2(2P16.1) MUTATED`
TCGA-FA-A4XK TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8061 
       23.28         8.15        14.04        35.54        31.73        27.35 
TCGA-FM-8000 TCGA-G8-6907 TCGA-G8-6909 TCGA-GS-A9TQ TCGA-GS-A9TX TCGA-GS-A9TY 
       31.96        19.56       116.81        32.28        45.14       109.58 
TCGA-GS-A9TZ TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.15         0.03         0.56 

$`AMP PEAK  2(2P16.1) 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-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       31.10        24.69         4.14        22.32         9.80        10.29 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       26.01        12.66        41.16        51.98        70.06       211.23 
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-A9U3 
       57.17        38.24       128.12        24.00        53.16       111.58 
TCGA-GS-A9U4 TCGA-RQ-A68N 
       12.85        25.91 

  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                         0.03                          1.91 
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                       116.81                        211.23 
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                       27.350                        28.555 
[1] "0.0 - 116.8 (27.4)" "1.9 - 211.2 (28.6)"
[1] "hr=" "2.6"
D2V2, continuous
D2V3, binary
                               cls
clus                             0  1
  AMP PEAK  2(2P16.1) MUTATED   10  5
  AMP PEAK  2(2P16.1) WILD-TYPE 16 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P16.1) MUTATED     10    5
  AMP PEAK  2(2P16.1) WILD-TYPE   16   16
        clus
vv       AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  FEMALE                          10                            16
  MALE                             5                            16
[1] 2 2
[1] FALSE
D2V4, binary
                               cls
clus                             0  1
  AMP PEAK  2(2P16.1) MUTATED   12  2
  AMP PEAK  2(2P16.1) WILD-TYPE 27  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P16.1) MUTATED     12    2
  AMP PEAK  2(2P16.1) WILD-TYPE   27    5
     clus
vv    AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  NO                           12                            27
  YES                           2                             5
[1] 2 2
[1] FALSE
                               vv
clus                            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  AMP PEAK  2(2P16.1) MUTATED                                                                                  11
  AMP PEAK  2(2P16.1) WILD-TYPE                                                                                29
                               vv
clus                            PRIMARY DLBCL OF THE CNS
  AMP PEAK  2(2P16.1) MUTATED                          2
  AMP PEAK  2(2P16.1) WILD-TYPE                        1
                               vv
clus                            PRIMARY MEDIASTINAL (THYMIC) DLBCL
  AMP PEAK  2(2P16.1) MUTATED                                    2
  AMP PEAK  2(2P16.1) WILD-TYPE                                  2
D2V5, multiclass
                                                                                   clus
vv                                                                                  AMP PEAK  2(2P16.1) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                          11
  PRIMARY DLBCL OF THE CNS                                                                                    2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                          2
                                                                                   clus
vv                                                                                  AMP PEAK  2(2P16.1) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                            29
  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
  AMP PEAK  2(2P16.1) MUTATED       6                         0     9
  AMP PEAK  2(2P16.1) WILD-TYPE    12                         1    19
D2V6, multiclass
                           clus
vv                          AMP PEAK  2(2P16.1) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               9
                           clus
vv                          AMP PEAK  2(2P16.1) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                               cls
clus                             0  1
  AMP PEAK  2(2P16.1) MUTATED    5 10
  AMP PEAK  2(2P16.1) WILD-TYPE  7 25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P16.1) MUTATED      5   10
  AMP PEAK  2(2P16.1) WILD-TYPE    7   25
                        clus
vv                       AMP PEAK  2(2P16.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          10
                        clus
vv                       AMP PEAK  2(2P16.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            25
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(3Q27.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  3(3Q27.3) MUTATED   13  1
  AMP PEAK  3(3Q27.3) WILD-TYPE 25  8
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                           14                            33 
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                            1                             8 
$`AMP PEAK  3(3Q27.3) MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-A7CW 
       23.28        24.62        14.04        18.18        31.10        26.01 
TCGA-G8-6914 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GS-A9TQ TCGA-GS-A9TW TCGA-GS-A9TX 
      196.60        51.98        43.86        32.28        53.16        45.14 
TCGA-GS-A9U3 TCGA-RQ-A68N 
      111.58        25.91 

$`AMP PEAK  3(3Q27.3) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FF-8041 
        4.34         4.34         1.91        23.64         8.15        35.54 
TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       31.73        24.69         4.14        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CX TCGA-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-A4D5 
      211.23        19.56       116.81       150.51        98.07        42.71 
TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TY TCGA-GS-A9TZ 
       57.17        38.24       128.12        24.00       109.58        25.15 
TCGA-GS-A9U4 TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85         0.03         0.56 

  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                        14.04                          0.03 
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                       196.60                        211.23 
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                        31.69                         25.15 
[1] "14.0 - 196.6 (31.7)" "0.0 - 211.2 (25.1)" 
[1] "hr=" "3.5"
D3V2, continuous
D3V3, binary
                               cls
clus                             0  1
  AMP PEAK  3(3Q27.3) MUTATED    9  5
  AMP PEAK  3(3Q27.3) WILD-TYPE 17 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q27.3) MUTATED      9    5
  AMP PEAK  3(3Q27.3) WILD-TYPE   17   16
        clus
vv       AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE
  FEMALE                           9                            17
  MALE                             5                            16
[1] 2 2
[1] FALSE
D3V4, binary
                               cls
clus                             0  1
  AMP PEAK  3(3Q27.3) MUTATED   12  2
  AMP PEAK  3(3Q27.3) WILD-TYPE 27  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q27.3) MUTATED     12    2
  AMP PEAK  3(3Q27.3) WILD-TYPE   27    5
     clus
vv    AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE
  NO                           12                            27
  YES                           2                             5
[1] 2 2
[1] FALSE
                               vv
clus                            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  AMP PEAK  3(3Q27.3) MUTATED                                                                                  12
  AMP PEAK  3(3Q27.3) WILD-TYPE                                                                                28
                               vv
clus                            PRIMARY DLBCL OF THE CNS
  AMP PEAK  3(3Q27.3) MUTATED                          1
  AMP PEAK  3(3Q27.3) WILD-TYPE                        2
                               vv
clus                            PRIMARY MEDIASTINAL (THYMIC) DLBCL
  AMP PEAK  3(3Q27.3) MUTATED                                    1
  AMP PEAK  3(3Q27.3) WILD-TYPE                                  3
D3V5, multiclass
                                                                                   clus
vv                                                                                  AMP PEAK  3(3Q27.3) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                          12
  PRIMARY DLBCL OF THE CNS                                                                                    1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                          1
                                                                                   clus
vv                                                                                  AMP PEAK  3(3Q27.3) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                            28
  PRIMARY DLBCL OF THE CNS                                                                                      2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                            3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(3Q27.3) MUTATED       6                         0     8
  AMP PEAK  3(3Q27.3) WILD-TYPE    12                         1    20
D3V6, multiclass
                           clus
vv                          AMP PEAK  3(3Q27.3) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               8
                           clus
vv                          AMP PEAK  3(3Q27.3) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                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"
D3V7, binary
                               cls
clus                             0  1
  AMP PEAK  3(3Q27.3) MUTATED    5  9
  AMP PEAK  3(3Q27.3) WILD-TYPE  7 26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q27.3) MUTATED      5    9
  AMP PEAK  3(3Q27.3) WILD-TYPE    7   26
                        clus
vv                       AMP PEAK  3(3Q27.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                           9
                        clus
vv                       AMP PEAK  3(3Q27.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            26
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(3Q29) MUTATION ANALYSIS
D4V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  4(3Q29) MUTATED   15  0
  AMP PEAK  4(3Q29) WILD-TYPE 23  9
  AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE 
                         15                          32 
  AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE 
                          0                           9 
$`AMP PEAK  4(3Q29) MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-A7CW TCGA-G8-6914 
       24.62        14.04        18.18        31.10        26.01       196.60 
TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GS-A9TQ TCGA-GS-A9TU TCGA-GS-A9TW TCGA-GS-A9TX 
       51.98        43.86        32.28       128.12        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9U3 TCGA-RQ-A68N 
      109.58       111.58        25.91 

$`AMP PEAK  4(3Q29) 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-8047 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
        9.80        10.29        12.66        31.96        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-7353 
       70.06       211.23        19.56       116.81       150.51        98.07 
TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TV TCGA-GS-A9TZ TCGA-GS-A9U4 
       42.71        57.17        38.24        24.00        25.15        12.85 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE 
                      14.04                        0.03 
  AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE 
                     196.60                      211.23 
  AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE 
                     43.860                      24.345 
[1] "14.0 - 196.6 (43.9)" "0.0 - 211.2 (24.3)" 
[1] "hr="     "4.2e+08"
D4V2, continuous
D4V3, binary
                             cls
clus                           0  1
  AMP PEAK  4(3Q29) MUTATED   10  5
  AMP PEAK  4(3Q29) WILD-TYPE 16 16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3Q29) MUTATED     10    5
  AMP PEAK  4(3Q29) WILD-TYPE   16   16
        clus
vv       AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE
  FEMALE                        10                          16
  MALE                           5                          16
[1] 2 2
[1] FALSE
D4V4, binary
                             cls
clus                           0  1
  AMP PEAK  4(3Q29) MUTATED   12  3
  AMP PEAK  4(3Q29) WILD-TYPE 27  4
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3Q29) MUTATED     12    3
  AMP PEAK  4(3Q29) WILD-TYPE   27    4
     clus
vv    AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE
  NO                         12                          27
  YES                         3                           4
[1] 2 2
[1] FALSE
                             vv
clus                          DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  AMP PEAK  4(3Q29) MUTATED                                                                                  13
  AMP PEAK  4(3Q29) WILD-TYPE                                                                                27
                             vv
clus                          PRIMARY DLBCL OF THE CNS
  AMP PEAK  4(3Q29) MUTATED                          1
  AMP PEAK  4(3Q29) WILD-TYPE                        2
                             vv
clus                          PRIMARY MEDIASTINAL (THYMIC) DLBCL
  AMP PEAK  4(3Q29) MUTATED                                    1
  AMP PEAK  4(3Q29) WILD-TYPE                                  3
D4V5, multiclass
                                                                                   clus
vv                                                                                  AMP PEAK  4(3Q29) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                        13
  PRIMARY DLBCL OF THE CNS                                                                                  1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                        1
                                                                                   clus
vv                                                                                  AMP PEAK  4(3Q29) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                          27
  PRIMARY DLBCL OF THE CNS                                                                                    2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                          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
  AMP PEAK  4(3Q29) MUTATED       5                         0    10
  AMP PEAK  4(3Q29) WILD-TYPE    13                         1    18
D4V6, multiclass
                           clus
vv                          AMP PEAK  4(3Q29) MUTATED
  ASIAN                                             5
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            10
                           clus
vv                          AMP PEAK  4(3Q29) WILD-TYPE
  ASIAN                                              13
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                             cls
clus                           0  1
  AMP PEAK  4(3Q29) MUTATED    7  8
  AMP PEAK  4(3Q29) WILD-TYPE  5 27
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3Q29) MUTATED      7    8
  AMP PEAK  4(3Q29) WILD-TYPE    5   27
                        clus
vv                       AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE
  HISPANIC OR LATINO                             7                           5
  NOT HISPANIC OR LATINO                         8                          27
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(5P13.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  5(5P13.1) MUTATED    6  2
  AMP PEAK  5(5P13.1) WILD-TYPE 32  7
  AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE 
                            8                            39 
  AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE 
                            2                             7 
$`AMP PEAK  5(5P13.1) MUTATED`
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-G8-6909 TCGA-GS-A9TW TCGA-GS-A9TX 
        8.15        14.04        35.54       116.81        53.16        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ 
      109.58        25.15 

$`AMP PEAK  5(5P13.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-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-G8-6914 
       41.16        51.98        70.06       211.23        19.56       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      150.51        98.07        51.98        42.71        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9U3 TCGA-GS-A9U4 
       32.28        38.24       128.12        24.00       111.58        12.85 
TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.91         0.03         0.56 

  AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE 
                         8.15                          0.03 
  AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE 
                       116.81                        211.23 
  AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE 
                        40.34                         26.01 
[1] "8.2 - 116.8 (40.3)" "0.0 - 211.2 (26.0)"
[1] "hr=" "1.4"
D5V2, continuous
D5V3, binary
                               cls
clus                             0  1
  AMP PEAK  5(5P13.1) MUTATED    5  3
  AMP PEAK  5(5P13.1) WILD-TYPE 21 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5P13.1) MUTATED      5    3
  AMP PEAK  5(5P13.1) WILD-TYPE   21   18
        clus
vv       AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE
  FEMALE                           5                            21
  MALE                             3                            18
[1] 2 2
[1] FALSE
D5V4, binary
                               cls
clus                             0  1
  AMP PEAK  5(5P13.1) MUTATED    5  3
  AMP PEAK  5(5P13.1) WILD-TYPE 34  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5P13.1) MUTATED      5    3
  AMP PEAK  5(5P13.1) WILD-TYPE   34    4
     clus
vv    AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE
  NO                            5                            34
  YES                           3                             4
[1] 2 2
[1] FALSE
                               vv
clus                            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  AMP PEAK  5(5P13.1) MUTATED                                                                                   5
  AMP PEAK  5(5P13.1) WILD-TYPE                                                                                35
                               vv
clus                            PRIMARY DLBCL OF THE CNS
  AMP PEAK  5(5P13.1) MUTATED                          0
  AMP PEAK  5(5P13.1) WILD-TYPE                        3
                               vv
clus                            PRIMARY MEDIASTINAL (THYMIC) DLBCL
  AMP PEAK  5(5P13.1) MUTATED                                    3
  AMP PEAK  5(5P13.1) WILD-TYPE                                  1
D5V5, multiclass
                                                                                   clus
vv                                                                                  AMP PEAK  5(5P13.1) 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                                                                                  AMP PEAK  5(5P13.1) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                            35
  PRIMARY DLBCL OF THE CNS                                                                                      3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                            1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(5P13.1) MUTATED       3                         0     5
  AMP PEAK  5(5P13.1) WILD-TYPE    15                         1    23
D5V6, multiclass
                           clus
vv                          AMP PEAK  5(5P13.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               5
                           clus
vv                          AMP PEAK  5(5P13.1) WILD-TYPE
  ASIAN                                                15
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                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"
D5V7, binary
                               cls
clus                             0  1
  AMP PEAK  5(5P13.1) MUTATED    4  4
  AMP PEAK  5(5P13.1) WILD-TYPE  8 31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5P13.1) MUTATED      4    4
  AMP PEAK  5(5P13.1) WILD-TYPE    8   31
                        clus
vv                       AMP PEAK  5(5P13.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                           4
                        clus
vv                       AMP PEAK  5(5P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                            31
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(7P22.3) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  6(7P22.3) MUTATED   15  1
  AMP PEAK  6(7P22.3) WILD-TYPE 23  8
  AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE 
                           16                            31 
  AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE 
                            1                             8 
$`AMP PEAK  6(7P22.3) 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-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GS-A9TQ 
      196.60       150.51        98.07        51.98        43.86        32.28 
TCGA-GS-A9TU TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9U3 
      128.12        45.14       109.58       111.58 

$`AMP PEAK  6(7P22.3) 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-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TT 
      211.23        19.56       116.81        42.71        57.17        38.24 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TZ TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
       24.00        53.16        25.15        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE 
                        14.04                          0.03 
  AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE 
                       196.60                        211.23 
  AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE 
                         44.5                          24.0 
[1] "14.0 - 196.6 (44.5)" "0.0 - 211.2 (24.0)" 
[1] "hr=" "6"  
D6V2, continuous
D6V3, binary
                               cls
clus                             0  1
  AMP PEAK  6(7P22.3) MUTATED   10  6
  AMP PEAK  6(7P22.3) WILD-TYPE 16 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P22.3) MUTATED     10    6
  AMP PEAK  6(7P22.3) WILD-TYPE   16   15
        clus
vv       AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE
  FEMALE                          10                            16
  MALE                             6                            15
[1] 2 2
[1] FALSE
D6V4, binary
                               cls
clus                             0  1
  AMP PEAK  6(7P22.3) MUTATED   13  3
  AMP PEAK  6(7P22.3) WILD-TYPE 26  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P22.3) MUTATED     13    3
  AMP PEAK  6(7P22.3) WILD-TYPE   26    4
     clus
vv    AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE
  NO                           13                            26
  YES                           3                             4
[1] 2 2
[1] FALSE
                               vv
clus                            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  AMP PEAK  6(7P22.3) MUTATED                                                                                  16
  AMP PEAK  6(7P22.3) WILD-TYPE                                                                                24
                               vv
clus                            PRIMARY DLBCL OF THE CNS
  AMP PEAK  6(7P22.3) MUTATED                          0
  AMP PEAK  6(7P22.3) WILD-TYPE                        3
                               vv
clus                            PRIMARY MEDIASTINAL (THYMIC) DLBCL
  AMP PEAK  6(7P22.3) MUTATED                                    0
  AMP PEAK  6(7P22.3) WILD-TYPE                                  4
D6V5, multiclass
                                                                                   clus
vv                                                                                  AMP PEAK  6(7P22.3) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                          16
  PRIMARY DLBCL OF THE CNS                                                                                    0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                          0
                                                                                   clus
vv                                                                                  AMP PEAK  6(7P22.3) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                            24
  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
  AMP PEAK  6(7P22.3) MUTATED       6                         0    10
  AMP PEAK  6(7P22.3) WILD-TYPE    12                         1    18
D6V6, multiclass
                           clus
vv                          AMP PEAK  6(7P22.3) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              10
                           clus
vv                          AMP PEAK  6(7P22.3) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                               cls
clus                             0  1
  AMP PEAK  6(7P22.3) MUTATED    5 11
  AMP PEAK  6(7P22.3) WILD-TYPE  7 24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P22.3) MUTATED      5   11
  AMP PEAK  6(7P22.3) WILD-TYPE    7   24
                        clus
vv                       AMP PEAK  6(7P22.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          11
                        clus
vv                       AMP PEAK  6(7P22.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            24
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(7Q21.3) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  7(7Q21.3) MUTATED   14  1
  AMP PEAK  7(7Q21.3) WILD-TYPE 24  8
  AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE 
                           15                            32 
  AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE 
                            1                             8 
$`AMP PEAK  7(7Q21.3) MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-A7CQ TCGA-FF-A7CW 
       23.28        24.62        14.04        31.10         9.80        26.01 
TCGA-FM-8000 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GS-A9TQ TCGA-GS-A9TU 
       31.96        98.07        51.98        43.86        32.28       128.12 
TCGA-GS-A9TX TCGA-GS-A9TY TCGA-RQ-AAAT 
       45.14       109.58         0.56 

$`AMP PEAK  7(7Q21.3) 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-A7CR TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       10.29        12.66        41.16        51.98        70.06       211.23 
TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D5 TCGA-GR-A4D9 
       19.56       116.81       196.60       150.51        42.71        57.17 
TCGA-GS-A9TT TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 
       38.24        24.00        53.16        25.15       111.58        12.85 
TCGA-RQ-A68N TCGA-RQ-A6JB 
       25.91         0.03 

  AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE 
                         0.56                          0.03 
  AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE 
                       128.12                        211.23 
  AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE 
                        31.96                         25.53 
[1] "0.6 - 128.1 (32.0)" "0.0 - 211.2 (25.5)"
[1] "hr=" "3.4"
D7V2, continuous
D7V3, binary
                               cls
clus                             0  1
  AMP PEAK  7(7Q21.3) MUTATED    9  6
  AMP PEAK  7(7Q21.3) WILD-TYPE 17 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q21.3) MUTATED      9    6
  AMP PEAK  7(7Q21.3) WILD-TYPE   17   15
        clus
vv       AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE
  FEMALE                           9                            17
  MALE                             6                            15
[1] 2 2
[1] FALSE
D7V4, binary
                               cls
clus                             0  1
  AMP PEAK  7(7Q21.3) MUTATED   13  2
  AMP PEAK  7(7Q21.3) WILD-TYPE 26  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q21.3) MUTATED     13    2
  AMP PEAK  7(7Q21.3) WILD-TYPE   26    5
     clus
vv    AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE
  NO                           13                            26
  YES                           2                             5
[1] 2 2
[1] FALSE
                               vv
clus                            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  AMP PEAK  7(7Q21.3) MUTATED                                                                                  14
  AMP PEAK  7(7Q21.3) WILD-TYPE                                                                                26
                               vv
clus                            PRIMARY DLBCL OF THE CNS
  AMP PEAK  7(7Q21.3) MUTATED                          1
  AMP PEAK  7(7Q21.3) WILD-TYPE                        2
                               vv
clus                            PRIMARY MEDIASTINAL (THYMIC) DLBCL
  AMP PEAK  7(7Q21.3) MUTATED                                    0
  AMP PEAK  7(7Q21.3) WILD-TYPE                                  4
D7V5, multiclass
                                                                                   clus
vv                                                                                  AMP PEAK  7(7Q21.3) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                          14
  PRIMARY DLBCL OF THE CNS                                                                                    1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                          0
                                                                                   clus
vv                                                                                  AMP PEAK  7(7Q21.3) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                            26
  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
  AMP PEAK  7(7Q21.3) MUTATED       7                         0     8
  AMP PEAK  7(7Q21.3) WILD-TYPE    11                         1    20
D7V6, multiclass
                           clus
vv                          AMP PEAK  7(7Q21.3) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               8
                           clus
vv                          AMP PEAK  7(7Q21.3) WILD-TYPE
  ASIAN                                                11
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                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"
D7V7, binary
                               cls
clus                             0  1
  AMP PEAK  7(7Q21.3) MUTATED    5 10
  AMP PEAK  7(7Q21.3) WILD-TYPE  7 25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q21.3) MUTATED      5   10
  AMP PEAK  7(7Q21.3) WILD-TYPE    7   25
                        clus
vv                       AMP PEAK  7(7Q21.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          10
                        clus
vv                       AMP PEAK  7(7Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            25
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(8Q24.23) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  8(8Q24.23) MUTATED   12  2
  AMP PEAK  8(8Q24.23) WILD-TYPE 26  7
  AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE 
                            14                             33 
  AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE 
                             2                              7 
$`AMP PEAK  8(8Q24.23) MUTATED`
TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
       24.62         8.15        18.18        35.54        31.10        31.73 
TCGA-FF-A7CQ TCGA-GR-7353 TCGA-GS-A9TQ TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TZ 
        9.80        98.07        32.28        53.16        45.14        25.15 
TCGA-GS-A9U3 TCGA-GS-A9U4 
      111.58        12.85 

$`AMP PEAK  8(8Q24.23) 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-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CR TCGA-FF-A7CW 
       24.69         4.14        27.35        22.32        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-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 

  AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE 
                          8.15                           0.03 
  AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE 
                        111.58                         211.23 
  AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE 
                        31.415                         26.010 
[1] "8.2 - 111.6 (31.4)" "0.0 - 211.2 (26.0)"
[1] "hr=" "1.1"
D8V2, continuous
D8V3, binary
                                cls
clus                              0  1
  AMP PEAK  8(8Q24.23) MUTATED   10  4
  AMP PEAK  8(8Q24.23) WILD-TYPE 16 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8Q24.23) MUTATED     10    4
  AMP PEAK  8(8Q24.23) WILD-TYPE   16   17
        clus
vv       AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE
  FEMALE                           10                             16
  MALE                              4                             17
[1] 2 2
[1] FALSE
D8V4, binary
                                cls
clus                              0  1
  AMP PEAK  8(8Q24.23) MUTATED   11  3
  AMP PEAK  8(8Q24.23) WILD-TYPE 28  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8Q24.23) MUTATED     11    3
  AMP PEAK  8(8Q24.23) WILD-TYPE   28    4
     clus
vv    AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE
  NO                            11                             28
  YES                            3                              4
[1] 2 2
[1] FALSE
                                vv
clus                             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  AMP PEAK  8(8Q24.23) MUTATED                                                                                  11
  AMP PEAK  8(8Q24.23) WILD-TYPE                                                                                29
                                vv
clus                             PRIMARY DLBCL OF THE CNS
  AMP PEAK  8(8Q24.23) MUTATED                          0
  AMP PEAK  8(8Q24.23) WILD-TYPE                        3
                                vv
clus                             PRIMARY MEDIASTINAL (THYMIC) DLBCL
  AMP PEAK  8(8Q24.23) MUTATED                                    3
  AMP PEAK  8(8Q24.23) WILD-TYPE                                  1
D8V5, multiclass
                                                                                   clus
vv                                                                                  AMP PEAK  8(8Q24.23) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                           11
  PRIMARY DLBCL OF THE CNS                                                                                     0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                           3
                                                                                   clus
vv                                                                                  AMP PEAK  8(8Q24.23) 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                                                                             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
  AMP PEAK  8(8Q24.23) MUTATED       6                         0     8
  AMP PEAK  8(8Q24.23) WILD-TYPE    12                         1    20
D8V6, multiclass
                           clus
vv                          AMP PEAK  8(8Q24.23) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                8
                           clus
vv                          AMP PEAK  8(8Q24.23) WILD-TYPE
  ASIAN                                                 12
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                                cls
clus                              0  1
  AMP PEAK  8(8Q24.23) MUTATED    6  8
  AMP PEAK  8(8Q24.23) WILD-TYPE  6 27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8Q24.23) MUTATED      6    8
  AMP PEAK  8(8Q24.23) WILD-TYPE    6   27
                        clus
vv                       AMP PEAK  8(8Q24.23) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                            8
                        clus
vv                       AMP PEAK  8(8Q24.23) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             27
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(12Q21.1) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  9(12Q21.1) MUTATED   11  3
  AMP PEAK  9(12Q21.1) WILD-TYPE 27  6
  AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE 
                            14                             33 
  AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE 
                             3                              6 
$`AMP PEAK  9(12Q21.1) MUTATED`
TCGA-FA-A4XK TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8043 
       23.28        23.64         8.15        14.04        35.54        31.73 
TCGA-FF-A7CR TCGA-GR-A4D5 TCGA-GS-A9TT TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
       10.29        42.71        38.24        45.14       109.58        25.15 
TCGA-RQ-A68N TCGA-RQ-AAAT 
       25.91         0.56 

$`AMP PEAK  9(12Q21.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A86F TCGA-FF-8042 
        4.34         4.34         1.91        24.62        18.18        31.10 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CW 
       24.69         4.14        27.35        22.32         9.80        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-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-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       43.86        57.17        32.28       128.12        24.00        53.16 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB 
      111.58        12.85         0.03 

  AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE 
                          0.56                           0.03 
  AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE 
                        109.58                         211.23 
  AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE 
                         25.53                          31.10 
[1] "0.6 - 109.6 (25.5)" "0.0 - 211.2 (31.1)"
[1] "hr=" "1.9"
D9V2, continuous
D9V3, binary
                                cls
clus                              0  1
  AMP PEAK  9(12Q21.1) MUTATED    8  6
  AMP PEAK  9(12Q21.1) WILD-TYPE 18 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12Q21.1) MUTATED      8    6
  AMP PEAK  9(12Q21.1) WILD-TYPE   18   15
        clus
vv       AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE
  FEMALE                            8                             18
  MALE                              6                             15
[1] 2 2
[1] FALSE
D9V4, binary
                                cls
clus                              0  1
  AMP PEAK  9(12Q21.1) MUTATED   11  3
  AMP PEAK  9(12Q21.1) WILD-TYPE 28  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12Q21.1) MUTATED     11    3
  AMP PEAK  9(12Q21.1) WILD-TYPE   28    4
     clus
vv    AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE
  NO                            11                             28
  YES                            3                              4
[1] 2 2
[1] FALSE
                                vv
clus                             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  AMP PEAK  9(12Q21.1) MUTATED                                                                                  10
  AMP PEAK  9(12Q21.1) WILD-TYPE                                                                                30
                                vv
clus                             PRIMARY DLBCL OF THE CNS
  AMP PEAK  9(12Q21.1) MUTATED                          2
  AMP PEAK  9(12Q21.1) WILD-TYPE                        1
                                vv
clus                             PRIMARY MEDIASTINAL (THYMIC) DLBCL
  AMP PEAK  9(12Q21.1) MUTATED                                    2
  AMP PEAK  9(12Q21.1) WILD-TYPE                                  2
D9V5, multiclass
                                                                                   clus
vv                                                                                  AMP PEAK  9(12Q21.1) 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                                                                           2
                                                                                   clus
vv                                                                                  AMP PEAK  9(12Q21.1) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                             30
  PRIMARY DLBCL OF THE CNS                                                                                       1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                             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
  AMP PEAK  9(12Q21.1) MUTATED       7                         0     7
  AMP PEAK  9(12Q21.1) WILD-TYPE    11                         1    21
D9V6, multiclass
                           clus
vv                          AMP PEAK  9(12Q21.1) MUTATED
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                7
                           clus
vv                          AMP PEAK  9(12Q21.1) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 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"
D9V7, binary
                                cls
clus                              0  1
  AMP PEAK  9(12Q21.1) MUTATED    6  8
  AMP PEAK  9(12Q21.1) WILD-TYPE  6 27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12Q21.1) MUTATED      6    8
  AMP PEAK  9(12Q21.1) WILD-TYPE    6   27
                        clus
vv                       AMP PEAK  9(12Q21.1) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                            8
                        clus
vv                       AMP PEAK  9(12Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             27
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 11(16P12.2) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 11(16P12.2) MUTATED    7  3
  AMP PEAK 11(16P12.2) WILD-TYPE 31  6
  AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE 
                            10                             37 
  AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE 
                             3                              6 
$`AMP PEAK 11(16P12.2) MUTATED`
TCGA-FA-A4XK TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8043 TCGA-FM-8000 TCGA-G8-6909 
       23.28         8.15        14.04        31.73        31.96       116.81 
TCGA-GR-A4D4 TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-RQ-A68N 
       51.98       109.58        25.15        25.91 

$`AMP PEAK 11(16P12.2) 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-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.10        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6325 
        9.80        10.29        26.01        12.66        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 
       70.06       211.23        19.56       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-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB 
       24.00        53.16        45.14       111.58        12.85         0.03 
TCGA-RQ-AAAT 
        0.56 

  AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE 
                          8.15                           0.03 
  AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE 
                        116.81                         211.23 
  AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE 
                         28.82                          27.35 
[1] "8.2 - 116.8 (28.8)" "0.0 - 211.2 (27.4)"
[1] "hr=" "2.1"
D10V2, continuous
D10V3, binary
                                cls
clus                              0  1
  AMP PEAK 11(16P12.2) MUTATED    6  4
  AMP PEAK 11(16P12.2) WILD-TYPE 20 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(16P12.2) MUTATED      6    4
  AMP PEAK 11(16P12.2) WILD-TYPE   20   17
        clus
vv       AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE
  FEMALE                            6                             20
  MALE                              4                             17
[1] 2 2
[1] FALSE
D10V4, binary
                                cls
clus                              0  1
  AMP PEAK 11(16P12.2) MUTATED    9  1
  AMP PEAK 11(16P12.2) WILD-TYPE 30  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(16P12.2) MUTATED      9    1
  AMP PEAK 11(16P12.2) WILD-TYPE   30    6
     clus
vv    AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE
  NO                             9                             30
  YES                            1                              6
[1] 2 2
[1] FALSE
                                vv
clus                             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  AMP PEAK 11(16P12.2) MUTATED                                                                                   8
  AMP PEAK 11(16P12.2) WILD-TYPE                                                                                32
                                vv
clus                             PRIMARY DLBCL OF THE CNS
  AMP PEAK 11(16P12.2) MUTATED                          1
  AMP PEAK 11(16P12.2) WILD-TYPE                        2
                                vv
clus                             PRIMARY MEDIASTINAL (THYMIC) DLBCL
  AMP PEAK 11(16P12.2) MUTATED                                    1
  AMP PEAK 11(16P12.2) WILD-TYPE                                  3
D10V5, multiclass
                                                                                   clus
vv                                                                                  AMP PEAK 11(16P12.2) 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                                                                                  AMP PEAK 11(16P12.2) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                             32
  PRIMARY DLBCL OF THE CNS                                                                                       2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(16P12.2) MUTATED       4                         0     6
  AMP PEAK 11(16P12.2) WILD-TYPE    14                         1    22
D10V6, multiclass
                           clus
vv                          AMP PEAK 11(16P12.2) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                6
                           clus
vv                          AMP PEAK 11(16P12.2) WILD-TYPE
  ASIAN                                                 14
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 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"
D10V7, binary
                                cls
clus                              0  1
  AMP PEAK 11(16P12.2) MUTATED    3  7
  AMP PEAK 11(16P12.2) WILD-TYPE  9 28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(16P12.2) MUTATED      3    7
  AMP PEAK 11(16P12.2) WILD-TYPE    9   28
                        clus
vv                       AMP PEAK 11(16P12.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                            7
                        clus
vv                       AMP PEAK 11(16P12.2) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                             28
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 12(18Q21.2) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 12(18Q21.2) MUTATED   14  2
  AMP PEAK 12(18Q21.2) WILD-TYPE 24  7
  AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE 
                            16                             31 
  AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE 
                             2                              7 
$`AMP PEAK 12(18Q21.2) MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8043 
       23.28        24.62        23.64        14.04        31.10        31.73 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-G8-6914 TCGA-GR-A4D6 TCGA-GS-A9TT 
        9.80        10.29        26.01       196.60        43.86        38.24 
TCGA-GS-A9TU TCGA-GS-A9TW TCGA-GS-A9U3 TCGA-RQ-AAAT 
      128.12        53.16       111.58         0.56 

$`AMP PEAK 12(18Q21.2) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A7Q1 TCGA-FA-A86F TCGA-FF-8041 
        4.34         4.34         1.91         8.15        18.18        35.54 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CX TCGA-FM-8000 
       24.69         4.14        27.35        22.32        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-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-A9TV TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U4 TCGA-RQ-A68N 
       24.00        45.14       109.58        25.15        12.85        25.91 
TCGA-RQ-A6JB 
        0.03 

  AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE 
                          0.56                           0.03 
  AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE 
                        196.60                         211.23 
  AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE 
                        28.555                         27.350 
[1] "0.6 - 196.6 (28.6)" "0.0 - 211.2 (27.4)"
[1] "hr=" "1.6"
D11V2, continuous
D11V3, binary
                                cls
clus                              0  1
  AMP PEAK 12(18Q21.2) MUTATED    9  7
  AMP PEAK 12(18Q21.2) WILD-TYPE 17 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(18Q21.2) MUTATED      9    7
  AMP PEAK 12(18Q21.2) WILD-TYPE   17   14
        clus
vv       AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE
  FEMALE                            9                             17
  MALE                              7                             14
[1] 2 2
[1] FALSE
D11V4, binary
                                cls
clus                              0  1
  AMP PEAK 12(18Q21.2) MUTATED   13  3
  AMP PEAK 12(18Q21.2) WILD-TYPE 26  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(18Q21.2) MUTATED     13    3
  AMP PEAK 12(18Q21.2) WILD-TYPE   26    4
     clus
vv    AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE
  NO                            13                             26
  YES                            3                              4
[1] 2 2
[1] FALSE
                                vv
clus                             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  AMP PEAK 12(18Q21.2) MUTATED                                                                                  14
  AMP PEAK 12(18Q21.2) WILD-TYPE                                                                                26
                                vv
clus                             PRIMARY DLBCL OF THE CNS
  AMP PEAK 12(18Q21.2) MUTATED                          1
  AMP PEAK 12(18Q21.2) WILD-TYPE                        2
                                vv
clus                             PRIMARY MEDIASTINAL (THYMIC) DLBCL
  AMP PEAK 12(18Q21.2) MUTATED                                    1
  AMP PEAK 12(18Q21.2) WILD-TYPE                                  3
D11V5, multiclass
                                                                                   clus
vv                                                                                  AMP PEAK 12(18Q21.2) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                           14
  PRIMARY DLBCL OF THE CNS                                                                                     1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                           1
                                                                                   clus
vv                                                                                  AMP PEAK 12(18Q21.2) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                             26
  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
  AMP PEAK 12(18Q21.2) MUTATED      10                         0     6
  AMP PEAK 12(18Q21.2) WILD-TYPE     8                         1    22
D11V6, multiclass
                           clus
vv                          AMP PEAK 12(18Q21.2) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                6
                           clus
vv                          AMP PEAK 12(18Q21.2) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 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"
D11V7, binary
                                cls
clus                              0  1
  AMP PEAK 12(18Q21.2) MUTATED    5 11
  AMP PEAK 12(18Q21.2) WILD-TYPE  7 24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(18Q21.2) MUTATED      5   11
  AMP PEAK 12(18Q21.2) WILD-TYPE    7   24
                        clus
vv                       AMP PEAK 12(18Q21.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           11
                        clus
vv                       AMP PEAK 12(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                             24
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 13(19Q13.43) MUTATION ANALYSIS
D12V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 13(19Q13.43) MUTATED    8  2
  AMP PEAK 13(19Q13.43) WILD-TYPE 30  7
  AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE 
                             10                              37 
  AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE 
                              2                               7 
$`AMP PEAK 13(19Q13.43) MUTATED`
TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-A7CR 
       24.62        23.64        14.04        18.18        35.54        10.29 
TCGA-G8-6909 TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TY 
      116.81        38.24       128.12       109.58 

$`AMP PEAK 13(19Q13.43) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7Q1 TCGA-FF-8042 
        4.34         4.34        23.28         1.91         8.15        31.10 
TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       31.73        24.69         4.14        27.35        22.32         9.80 
TCGA-FF-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-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 
      211.23        19.56       196.60       150.51        98.07        51.98 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TV TCGA-GS-A9TW 
       42.71        43.86        57.17        32.28        24.00        53.16 
TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
       45.14        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE 
                          10.29                            0.03 
  AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE 
                         128.12                          211.23 
  AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE 
                          30.08                           27.35 
[1] "10.3 - 128.1 (30.1)" "0.0 - 211.2 (27.4)" 
[1] "hr=" "1"  
D12V2, continuous
D12V3, binary
                                 cls
clus                               0  1
  AMP PEAK 13(19Q13.43) MUTATED    6  4
  AMP PEAK 13(19Q13.43) WILD-TYPE 20 17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(19Q13.43) MUTATED      6    4
  AMP PEAK 13(19Q13.43) WILD-TYPE   20   17
        clus
vv       AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE
  FEMALE                             6                              20
  MALE                               4                              17
[1] 2 2
[1] FALSE
D12V4, binary
                                 cls
clus                               0  1
  AMP PEAK 13(19Q13.43) MUTATED    8  2
  AMP PEAK 13(19Q13.43) WILD-TYPE 31  5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(19Q13.43) MUTATED      8    2
  AMP PEAK 13(19Q13.43) WILD-TYPE   31    5
     clus
vv    AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE
  NO                              8                              31
  YES                             2                               5
[1] 2 2
[1] FALSE
                                 vv
clus                              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  AMP PEAK 13(19Q13.43) MUTATED                                                                                   9
  AMP PEAK 13(19Q13.43) WILD-TYPE                                                                                31
                                 vv
clus                              PRIMARY DLBCL OF THE CNS
  AMP PEAK 13(19Q13.43) MUTATED                          0
  AMP PEAK 13(19Q13.43) WILD-TYPE                        3
                                 vv
clus                              PRIMARY MEDIASTINAL (THYMIC) DLBCL
  AMP PEAK 13(19Q13.43) MUTATED                                    1
  AMP PEAK 13(19Q13.43) WILD-TYPE                                  3
D12V5, multiclass
                                                                                   clus
vv                                                                                  AMP PEAK 13(19Q13.43) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                             9
  PRIMARY DLBCL OF THE CNS                                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                            1
                                                                                   clus
vv                                                                                  AMP PEAK 13(19Q13.43) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                              31
  PRIMARY DLBCL OF THE CNS                                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(19Q13.43) MUTATED       5                         0     5
  AMP PEAK 13(19Q13.43) WILD-TYPE    13                         1    23
D12V6, multiclass
                           clus
vv                          AMP PEAK 13(19Q13.43) MUTATED
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                 5
                           clus
vv                          AMP PEAK 13(19Q13.43) WILD-TYPE
  ASIAN                                                  13
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  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"
D12V7, binary
                                 cls
clus                               0  1
  AMP PEAK 13(19Q13.43) MUTATED    3  7
  AMP PEAK 13(19Q13.43) WILD-TYPE  9 28
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(19Q13.43) MUTATED      3    7
  AMP PEAK 13(19Q13.43) WILD-TYPE    9   28
                        clus
vv                       AMP PEAK 13(19Q13.43) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                             7
                        clus
vv                       AMP PEAK 13(19Q13.43) WILD-TYPE
  HISPANIC OR LATINO                                   9
  NOT HISPANIC OR LATINO                              28
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 14(XQ27.3) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 14(XQ27.3) MUTATED    5  2
  AMP PEAK 14(XQ27.3) WILD-TYPE 33  7
  AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE 
                            7                            40 
  AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE 
                            2                             7 
$`AMP PEAK 14(XQ27.3) MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-RQ-A68N 
       23.28         1.91        35.54        31.10        31.73        25.91 
TCGA-RQ-AAAT 
        0.56 

$`AMP PEAK 14(XQ27.3) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34         4.34        24.62        23.64         8.15        14.04 
TCGA-FA-A86F TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       18.18        24.69         4.14        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
       10.29        26.01        12.66        31.96        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       70.06       211.23        19.56       116.81       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       98.07        51.98        42.71        43.86        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       38.24       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB 
       25.15       111.58        12.85         0.03 

  AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE 
                         0.56                          0.03 
  AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE 
                        35.54                        211.23 
  AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE 
                       25.910                        29.655 
[1] "0.6 - 35.5 (25.9)"  "0.0 - 211.2 (29.7)"
[1] "hr=" "3.2"
D13V2, continuous
D13V3, binary
                               cls
clus                             0  1
  AMP PEAK 14(XQ27.3) MUTATED    4  3
  AMP PEAK 14(XQ27.3) WILD-TYPE 22 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(XQ27.3) MUTATED      4    3
  AMP PEAK 14(XQ27.3) WILD-TYPE   22   18
        clus
vv       AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE
  FEMALE                           4                            22
  MALE                             3                            18
[1] 2 2
[1] FALSE
D13V4, binary
                               cls
clus                             0  1
  AMP PEAK 14(XQ27.3) MUTATED    7  0
  AMP PEAK 14(XQ27.3) WILD-TYPE 32  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(XQ27.3) MUTATED      7    0
  AMP PEAK 14(XQ27.3) WILD-TYPE   32    7
     clus
vv    AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE
  NO                            7                            32
  YES                           0                             7
[1] 2 2
[1] FALSE
                               vv
clus                            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  AMP PEAK 14(XQ27.3) MUTATED                                                                                   4
  AMP PEAK 14(XQ27.3) WILD-TYPE                                                                                36
                               vv
clus                            PRIMARY DLBCL OF THE CNS
  AMP PEAK 14(XQ27.3) MUTATED                          2
  AMP PEAK 14(XQ27.3) WILD-TYPE                        1
                               vv
clus                            PRIMARY MEDIASTINAL (THYMIC) DLBCL
  AMP PEAK 14(XQ27.3) MUTATED                                    1
  AMP PEAK 14(XQ27.3) WILD-TYPE                                  3
D13V5, multiclass
                                                                                   clus
vv                                                                                  AMP PEAK 14(XQ27.3) 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                                                                                  AMP PEAK 14(XQ27.3) 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                                                                            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
  AMP PEAK 14(XQ27.3) MUTATED       5                         0     2
  AMP PEAK 14(XQ27.3) WILD-TYPE    13                         1    26
D13V6, multiclass
                           clus
vv                          AMP PEAK 14(XQ27.3) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               2
                           clus
vv                          AMP PEAK 14(XQ27.3) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                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"
D13V7, binary
                               cls
clus                             0  1
  AMP PEAK 14(XQ27.3) MUTATED    2  5
  AMP PEAK 14(XQ27.3) WILD-TYPE 10 30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(XQ27.3) MUTATED      2    5
  AMP PEAK 14(XQ27.3) WILD-TYPE   10   30
                        clus
vv                       AMP PEAK 14(XQ27.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                           5
                        clus
vv                       AMP PEAK 14(XQ27.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                            30
[1] 2 2
[1] FALSE

Clustering(14) Variable = DEL PEAK  1(1P36.32) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.32) MUTATED    9  2
  DEL PEAK  1(1P36.32) WILD-TYPE 29  7
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            11                             36 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                             2                              7 
$`DEL PEAK  1(1P36.32) MUTATED`
TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FM-8000 TCGA-G8-6325 TCGA-G8-6909 
       24.62         8.15        14.04        31.96        51.98       116.81 
TCGA-GR-7353 TCGA-GS-A9TQ TCGA-GS-A9TU TCGA-GS-A9TX TCGA-RQ-A68N 
       98.07        32.28       128.12        45.14        25.91 

$`DEL PEAK  1(1P36.32) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A86F 
        4.34         4.34        23.28         1.91        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-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D4 
       70.06       211.23        19.56       196.60       150.51        51.98 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TV TCGA-GS-A9TW 
       42.71        43.86        57.17        38.24        24.00        53.16 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB TCGA-RQ-AAAT 
      109.58        25.15       111.58        12.85         0.03         0.56 

  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                          8.15                           0.03 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                        128.12                         211.23 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                         32.28                          25.58 
[1] "8.2 - 128.1 (32.3)" "0.0 - 211.2 (25.6)"
[1] "hr=" "1.2"
D14V2, continuous
D14V3, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.32) MUTATED    5  6
  DEL PEAK  1(1P36.32) WILD-TYPE 21 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED      5    6
  DEL PEAK  1(1P36.32) WILD-TYPE   21   15
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  FEMALE                            5                             21
  MALE                              6                             15
[1] 2 2
[1] FALSE
D14V4, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.32) MUTATED    9  2
  DEL PEAK  1(1P36.32) WILD-TYPE 30  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED      9    2
  DEL PEAK  1(1P36.32) WILD-TYPE   30    5
     clus
vv    DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  NO                             9                             30
  YES                            2                              5
[1] 2 2
[1] FALSE
                                vv
clus                             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK  1(1P36.32) MUTATED                                                                                  10
  DEL PEAK  1(1P36.32) WILD-TYPE                                                                                30
                                vv
clus                             PRIMARY DLBCL OF THE CNS
  DEL PEAK  1(1P36.32) MUTATED                          1
  DEL PEAK  1(1P36.32) WILD-TYPE                        2
                                vv
clus                             PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK  1(1P36.32) MUTATED                                    0
  DEL PEAK  1(1P36.32) WILD-TYPE                                  4
D14V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK  1(1P36.32) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                           10
  PRIMARY DLBCL OF THE CNS                                                                                     1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                           0
                                                                                   clus
vv                                                                                  DEL PEAK  1(1P36.32) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                             30
  PRIMARY DLBCL OF THE CNS                                                                                       2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.32) MUTATED       3                         0     8
  DEL PEAK  1(1P36.32) WILD-TYPE    15                         1    20
D14V6, multiclass
                           clus
vv                          DEL PEAK  1(1P36.32) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                8
                           clus
vv                          DEL PEAK  1(1P36.32) WILD-TYPE
  ASIAN                                                 15
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 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"
D14V7, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.32) MUTATED    4  7
  DEL PEAK  1(1P36.32) WILD-TYPE  8 28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED      4    7
  DEL PEAK  1(1P36.32) WILD-TYPE    8   28
                        clus
vv                       DEL PEAK  1(1P36.32) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                            7
                        clus
vv                       DEL PEAK  1(1P36.32) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                             28
[1] 2 2
[1] FALSE

Clustering(15) Variable = DEL PEAK  2(1P13.1) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(1P13.1) MUTATED    8  3
  DEL PEAK  2(1P13.1) WILD-TYPE 30  6
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                           11                            36 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                            3                             6 
$`DEL PEAK  2(1P13.1) MUTATED`
TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-G8-6325 
        1.91        24.62        23.64         9.80        10.29        51.98 
TCGA-G8-6909 TCGA-GR-7353 TCGA-GR-A4D6 TCGA-GS-A9TQ TCGA-RQ-A68N 
      116.81        98.07        43.86        32.28        25.91 

$`DEL PEAK  2(1P13.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F 
        4.34         4.34        23.28         8.15        14.04        18.18 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       35.54        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6326 
       22.32        26.01        12.66        31.96        41.16        70.06 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GR-A4D5 
      211.23        19.56       196.60       150.51        51.98        42.71 
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-A6JB TCGA-RQ-AAAT 
      109.58        25.15       111.58        12.85         0.03         0.56 

  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                         1.91                          0.03 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                       116.81                        211.23 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                       25.910                        29.225 
[1] "1.9 - 116.8 (25.9)" "0.0 - 211.2 (29.2)"
[1] "hr=" "2"  
D15V2, continuous
D15V3, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.1) MUTATED    4  7
  DEL PEAK  2(1P13.1) WILD-TYPE 22 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      4    7
  DEL PEAK  2(1P13.1) WILD-TYPE   22   14
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  FEMALE                           4                            22
  MALE                             7                            14
[1] 2 2
[1] FALSE
D15V4, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.1) MUTATED   11  0
  DEL PEAK  2(1P13.1) WILD-TYPE 28  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED     11    0
  DEL PEAK  2(1P13.1) WILD-TYPE   28    7
     clus
vv    DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  NO                           11                            28
  YES                           0                             7
[1] 2 2
[1] FALSE
                               vv
clus                            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK  2(1P13.1) MUTATED                                                                                  10
  DEL PEAK  2(1P13.1) WILD-TYPE                                                                                30
                               vv
clus                            PRIMARY DLBCL OF THE CNS
  DEL PEAK  2(1P13.1) MUTATED                          1
  DEL PEAK  2(1P13.1) WILD-TYPE                        2
                               vv
clus                            PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK  2(1P13.1) MUTATED                                    0
  DEL PEAK  2(1P13.1) WILD-TYPE                                  4
D15V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK  2(1P13.1) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                          10
  PRIMARY DLBCL OF THE CNS                                                                                    1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                          0
                                                                                   clus
vv                                                                                  DEL PEAK  2(1P13.1) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                            30
  PRIMARY DLBCL OF THE CNS                                                                                      2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                            4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P13.1) MUTATED       6                         0     5
  DEL PEAK  2(1P13.1) WILD-TYPE    12                         1    23
D15V6, multiclass
                           clus
vv                          DEL PEAK  2(1P13.1) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               5
                           clus
vv                          DEL PEAK  2(1P13.1) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                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"
D15V7, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.1) MUTATED    2  9
  DEL PEAK  2(1P13.1) WILD-TYPE 10 26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      2    9
  DEL PEAK  2(1P13.1) WILD-TYPE   10   26
                        clus
vv                       DEL PEAK  2(1P13.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                           9
                        clus
vv                       DEL PEAK  2(1P13.1) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                            26
[1] 2 2
[1] FALSE

Clustering(16) Variable = DEL PEAK  3(1Q43) MUTATION ANALYSIS
D16V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  3(1Q43) MUTATED    9  1
  DEL PEAK  3(1Q43) WILD-TYPE 29  8
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         10                          37 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                          1                           8 
$`DEL PEAK  3(1Q43) MUTATED`
TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 
        1.91        24.62        18.18        31.10        31.73         4.14 
TCGA-FF-A7CW TCGA-GR-A4D9 TCGA-RQ-A68N TCGA-RQ-AAAT 
       26.01        57.17        25.91         0.56 

$`DEL PEAK  3(1Q43) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34         4.34        23.28        23.64         8.15        14.04 
TCGA-FF-8041 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       35.54        24.69        27.35        22.32         9.80        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-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-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV 
       42.71        43.86        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 
        0.03 

  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                       0.56                        0.03 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                      57.17                      211.23 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                     25.265                      32.280 
[1] "0.6 - 57.2 (25.3)"  "0.0 - 211.2 (32.3)"
[1] "hr=" "1.2"
D16V2, continuous
D16V3, binary
                             cls
clus                           0  1
  DEL PEAK  3(1Q43) MUTATED    7  3
  DEL PEAK  3(1Q43) WILD-TYPE 19 18
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED      7    3
  DEL PEAK  3(1Q43) WILD-TYPE   19   18
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  FEMALE                         7                          19
  MALE                           3                          18
[1] 2 2
[1] FALSE
D16V4, binary
                             cls
clus                           0  1
  DEL PEAK  3(1Q43) MUTATED   10  0
  DEL PEAK  3(1Q43) WILD-TYPE 29  7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED     10    0
  DEL PEAK  3(1Q43) WILD-TYPE   29    7
     clus
vv    DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  NO                         10                          29
  YES                         0                           7
[1] 2 2
[1] FALSE
                             vv
clus                          DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK  3(1Q43) MUTATED                                                                                   8
  DEL PEAK  3(1Q43) WILD-TYPE                                                                                32
                             vv
clus                          PRIMARY DLBCL OF THE CNS
  DEL PEAK  3(1Q43) MUTATED                          2
  DEL PEAK  3(1Q43) WILD-TYPE                        1
                             vv
clus                          PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK  3(1Q43) MUTATED                                    0
  DEL PEAK  3(1Q43) WILD-TYPE                                  4
D16V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK  3(1Q43) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                         8
  PRIMARY DLBCL OF THE CNS                                                                                  2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                        0
                                                                                   clus
vv                                                                                  DEL PEAK  3(1Q43) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                          32
  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
  DEL PEAK  3(1Q43) MUTATED       6                         0     4
  DEL PEAK  3(1Q43) WILD-TYPE    12                         1    24
D16V6, multiclass
                           clus
vv                          DEL PEAK  3(1Q43) MUTATED
  ASIAN                                             6
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                             4
                           clus
vv                          DEL PEAK  3(1Q43) WILD-TYPE
  ASIAN                                              12
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              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"
D16V7, binary
                             cls
clus                           0  1
  DEL PEAK  3(1Q43) MUTATED    2  8
  DEL PEAK  3(1Q43) WILD-TYPE 10 27
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED      2    8
  DEL PEAK  3(1Q43) WILD-TYPE   10   27
                        clus
vv                       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  HISPANIC OR LATINO                             2                          10
  NOT HISPANIC OR LATINO                         8                          27
[1] 2 2
[1] FALSE

Clustering(17) Variable = DEL PEAK  4(2Q23.1) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(2Q23.1) MUTATED    7  1
  DEL PEAK  4(2Q23.1) WILD-TYPE 31  8
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                            8                            39 
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                            1                             8 
$`DEL PEAK  4(2Q23.1) MUTATED`
TCGA-FA-A6HO TCGA-FF-8043 TCGA-FF-8047 TCGA-G8-6324 TCGA-GR-7351 TCGA-GS-A9TQ 
       24.62        31.73         4.14        41.16       150.51        32.28 
TCGA-GS-A9TX TCGA-RQ-A68N 
       45.14        25.91 

$`DEL PEAK  4(2Q23.1) 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-G8-6325 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-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT 
       98.07        51.98        42.71        43.86        57.17        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 
      128.12        24.00        53.16       109.58        25.15       111.58 
TCGA-GS-A9U4 TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85         0.03         0.56 

  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                         4.14                          0.03 
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                       150.51                        211.23 
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                       32.005                        26.010 
[1] "4.1 - 150.5 (32.0)" "0.0 - 211.2 (26.0)"
[1] "hr=" "1.6"
D17V2, continuous
D17V3, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q23.1) MUTATED    6  2
  DEL PEAK  4(2Q23.1) WILD-TYPE 20 19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q23.1) MUTATED      6    2
  DEL PEAK  4(2Q23.1) WILD-TYPE   20   19
        clus
vv       DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE
  FEMALE                           6                            20
  MALE                             2                            19
[1] 2 2
[1] FALSE
D17V4, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q23.1) MUTATED    6  2
  DEL PEAK  4(2Q23.1) WILD-TYPE 33  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q23.1) MUTATED      6    2
  DEL PEAK  4(2Q23.1) WILD-TYPE   33    5
     clus
vv    DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE
  NO                            6                            33
  YES                           2                             5
[1] 2 2
[1] FALSE
                               vv
clus                            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK  4(2Q23.1) MUTATED                                                                                   7
  DEL PEAK  4(2Q23.1) WILD-TYPE                                                                                33
                               vv
clus                            PRIMARY DLBCL OF THE CNS
  DEL PEAK  4(2Q23.1) MUTATED                          1
  DEL PEAK  4(2Q23.1) WILD-TYPE                        2
                               vv
clus                            PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK  4(2Q23.1) MUTATED                                    0
  DEL PEAK  4(2Q23.1) WILD-TYPE                                  4
D17V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK  4(2Q23.1) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                           7
  PRIMARY DLBCL OF THE CNS                                                                                    1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                          0
                                                                                   clus
vv                                                                                  DEL PEAK  4(2Q23.1) 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                                                                            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
  DEL PEAK  4(2Q23.1) MUTATED       3                         1     4
  DEL PEAK  4(2Q23.1) WILD-TYPE    15                         0    24
D17V6, multiclass
                           clus
vv                          DEL PEAK  4(2Q23.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                               4
                           clus
vv                          DEL PEAK  4(2Q23.1) WILD-TYPE
  ASIAN                                                15
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                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"
D17V7, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q23.1) MUTATED    3  5
  DEL PEAK  4(2Q23.1) WILD-TYPE  9 30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q23.1) MUTATED      3    5
  DEL PEAK  4(2Q23.1) WILD-TYPE    9   30
                        clus
vv                       DEL PEAK  4(2Q23.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                           5
                        clus
vv                       DEL PEAK  4(2Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                            30
[1] 2 2
[1] FALSE

Clustering(18) Variable = DEL PEAK  5(3P21.31) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  5(3P21.31) MUTATED    7  1
  DEL PEAK  5(3P21.31) WILD-TYPE 31  8
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                             8                             39 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                             1                              8 
$`DEL PEAK  5(3P21.31) MUTATED`
TCGA-FA-8693 TCGA-FA-A86F TCGA-FF-A7CR TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TZ 
        4.34        18.18        10.29        32.28        38.24        25.15 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

$`DEL PEAK  5(3P21.31) WILD-TYPE`
TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34        23.28         1.91        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-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-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       27.35        22.32         9.80        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-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY 
       57.17       128.12        24.00        53.16        45.14       109.58 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N 
      111.58        12.85        25.91 

  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                          0.03                           1.91 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                         38.24                         211.23 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                        14.235                         31.730 
[1] "0.0 - 38.2 (14.2)"  "1.9 - 211.2 (31.7)"
[1] "hr=" "1.6"
D18V2, continuous
D18V3, binary
                                cls
clus                              0  1
  DEL PEAK  5(3P21.31) MUTATED    4  4
  DEL PEAK  5(3P21.31) WILD-TYPE 22 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED      4    4
  DEL PEAK  5(3P21.31) WILD-TYPE   22   17
        clus
vv       DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  FEMALE                            4                             22
  MALE                              4                             17
[1] 2 2
[1] FALSE
D18V4, binary
                                cls
clus                              0  1
  DEL PEAK  5(3P21.31) MUTATED    5  2
  DEL PEAK  5(3P21.31) WILD-TYPE 34  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED      5    2
  DEL PEAK  5(3P21.31) WILD-TYPE   34    5
     clus
vv    DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  NO                             5                             34
  YES                            2                              5
[1] 2 2
[1] FALSE
                                vv
clus                             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK  5(3P21.31) MUTATED                                                                                   5
  DEL PEAK  5(3P21.31) WILD-TYPE                                                                                35
                                vv
clus                             PRIMARY DLBCL OF THE CNS
  DEL PEAK  5(3P21.31) MUTATED                          2
  DEL PEAK  5(3P21.31) WILD-TYPE                        1
                                vv
clus                             PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK  5(3P21.31) MUTATED                                    1
  DEL PEAK  5(3P21.31) WILD-TYPE                                  3
D18V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK  5(3P21.31) 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                                                                           1
                                                                                   clus
vv                                                                                  DEL PEAK  5(3P21.31) 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
  DEL PEAK  5(3P21.31) MUTATED       1                         0     7
  DEL PEAK  5(3P21.31) WILD-TYPE    17                         1    21
D18V6, multiclass
                           clus
vv                          DEL PEAK  5(3P21.31) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                7
                           clus
vv                          DEL PEAK  5(3P21.31) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 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"
D18V7, binary
                                cls
clus                              0  1
  DEL PEAK  5(3P21.31) MUTATED    4  4
  DEL PEAK  5(3P21.31) WILD-TYPE  8 31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED      4    4
  DEL PEAK  5(3P21.31) WILD-TYPE    8   31
                        clus
vv                       DEL PEAK  5(3P21.31) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                            4
                        clus
vv                       DEL PEAK  5(3P21.31) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                             31
[1] 2 2
[1] FALSE

Clustering(19) Variable = DEL PEAK  6(4Q35.1) MUTATION ANALYSIS
D19V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(4Q35.1) MUTATED    8  2
  DEL PEAK  6(4Q35.1) WILD-TYPE 30  7
  DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE 
                           10                            37 
  DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE 
                            2                             7 
$`DEL PEAK  6(4Q35.1) MUTATED`
TCGA-FA-A6HN TCGA-FA-A86F TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-A7CQ 
        1.91        18.18        31.10        31.73         4.14         9.80 
TCGA-FF-A7CR TCGA-GR-7353 TCGA-GS-A9TQ TCGA-GS-A9TW 
       10.29        98.07        32.28        53.16 

$`DEL PEAK  6(4Q35.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        23.28        24.62        23.64         8.15 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CW 
       14.04        35.54        24.69        27.35        22.32        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-A9TX 
       43.86        57.17        38.24       128.12        24.00        45.14 
TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
      109.58        25.15       111.58        12.85        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

  DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE 
                         1.91                          0.03 
  DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE 
                        98.07                        211.23 
  DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE 
                        24.64                         27.35 
[1] "1.9 - 98.1 (24.6)"  "0.0 - 211.2 (27.4)"
[1] "hr=" "2"  
D19V2, continuous
D19V3, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q35.1) MUTATED    6  4
  DEL PEAK  6(4Q35.1) WILD-TYPE 20 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q35.1) MUTATED      6    4
  DEL PEAK  6(4Q35.1) WILD-TYPE   20   17
        clus
vv       DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE
  FEMALE                           6                            20
  MALE                             4                            17
[1] 2 2
[1] FALSE
D19V4, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q35.1) MUTATED    9  1
  DEL PEAK  6(4Q35.1) WILD-TYPE 30  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q35.1) MUTATED      9    1
  DEL PEAK  6(4Q35.1) WILD-TYPE   30    6
     clus
vv    DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE
  NO                            9                            30
  YES                           1                             6
[1] 2 2
[1] FALSE
                               vv
clus                            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK  6(4Q35.1) MUTATED                                                                                   9
  DEL PEAK  6(4Q35.1) WILD-TYPE                                                                                31
                               vv
clus                            PRIMARY DLBCL OF THE CNS
  DEL PEAK  6(4Q35.1) MUTATED                          0
  DEL PEAK  6(4Q35.1) WILD-TYPE                        3
                               vv
clus                            PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK  6(4Q35.1) MUTATED                                    1
  DEL PEAK  6(4Q35.1) WILD-TYPE                                  3
D19V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK  6(4Q35.1) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                           9
  PRIMARY DLBCL OF THE CNS                                                                                    0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                          1
                                                                                   clus
vv                                                                                  DEL PEAK  6(4Q35.1) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                            31
  PRIMARY DLBCL OF THE CNS                                                                                      3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                            3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(4Q35.1) MUTATED       6                         0     4
  DEL PEAK  6(4Q35.1) WILD-TYPE    12                         1    24
D19V6, multiclass
                           clus
vv                          DEL PEAK  6(4Q35.1) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               4
                           clus
vv                          DEL PEAK  6(4Q35.1) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                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"
D19V7, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q35.1) MUTATED    2  8
  DEL PEAK  6(4Q35.1) WILD-TYPE 10 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q35.1) MUTATED      2    8
  DEL PEAK  6(4Q35.1) WILD-TYPE   10   27
                        clus
vv                       DEL PEAK  6(4Q35.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                           8
                        clus
vv                       DEL PEAK  6(4Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                            27
[1] 2 2
[1] FALSE

Clustering(20) Variable = DEL PEAK  7(5Q33.3) MUTATION ANALYSIS
D20V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  7(5Q33.3) MUTATED    3  1
  DEL PEAK  7(5Q33.3) WILD-TYPE 35  8
  DEL PEAK  7(5Q33.3) MUTATED DEL PEAK  7(5Q33.3) WILD-TYPE 
                            4                            43 
  DEL PEAK  7(5Q33.3) MUTATED DEL PEAK  7(5Q33.3) WILD-TYPE 
                            1                             8 
$`DEL PEAK  7(5Q33.3) MUTATED`
TCGA-FA-A4XK TCGA-GR-7353 TCGA-RQ-A6JB TCGA-RQ-AAAT 
       23.28        98.07         0.03         0.56 

$`DEL PEAK  7(5Q33.3) 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-G8-6325 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-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV 
       43.86        57.17        32.28        38.24       128.12        24.00 
TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 
       53.16        45.14       109.58        25.15       111.58        12.85 
TCGA-RQ-A68N 
       25.91 

  DEL PEAK  7(5Q33.3) MUTATED DEL PEAK  7(5Q33.3) WILD-TYPE 
                         0.03                          1.91 
  DEL PEAK  7(5Q33.3) MUTATED DEL PEAK  7(5Q33.3) WILD-TYPE 
                        98.07                        211.23 
  DEL PEAK  7(5Q33.3) MUTATED DEL PEAK  7(5Q33.3) WILD-TYPE 
                        11.92                         31.10 
[1] "0.0 - 98.1 (11.9)"  "1.9 - 211.2 (31.1)"
[1] "hr=" "2.9"
D20V2, continuous
D20V3, binary
                               cls
clus                             0  1
  DEL PEAK  7(5Q33.3) MUTATED    2  2
  DEL PEAK  7(5Q33.3) WILD-TYPE 24 19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5Q33.3) MUTATED      2    2
  DEL PEAK  7(5Q33.3) WILD-TYPE   24   19
        clus
vv       DEL PEAK  7(5Q33.3) MUTATED DEL PEAK  7(5Q33.3) WILD-TYPE
  FEMALE                           2                            24
  MALE                             2                            19
[1] 2 2
[1] FALSE
D20V4, binary
                               cls
clus                             0  1
  DEL PEAK  7(5Q33.3) MUTATED    3  0
  DEL PEAK  7(5Q33.3) WILD-TYPE 36  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5Q33.3) MUTATED      3    0
  DEL PEAK  7(5Q33.3) WILD-TYPE   36    7
     clus
vv    DEL PEAK  7(5Q33.3) MUTATED DEL PEAK  7(5Q33.3) WILD-TYPE
  NO                            3                            36
  YES                           0                             7
[1] 2 2
[1] FALSE
                               vv
clus                            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK  7(5Q33.3) MUTATED                                                                                   2
  DEL PEAK  7(5Q33.3) WILD-TYPE                                                                                38
                               vv
clus                            PRIMARY DLBCL OF THE CNS
  DEL PEAK  7(5Q33.3) MUTATED                          2
  DEL PEAK  7(5Q33.3) WILD-TYPE                        1
                               vv
clus                            PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK  7(5Q33.3) MUTATED                                    0
  DEL PEAK  7(5Q33.3) WILD-TYPE                                  4
D20V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK  7(5Q33.3) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                           2
  PRIMARY DLBCL OF THE CNS                                                                                    2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                          0
                                                                                   clus
vv                                                                                  DEL PEAK  7(5Q33.3) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                            38
  PRIMARY DLBCL OF THE CNS                                                                                      1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                            4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(5Q33.3) MUTATED       1                         0     3
  DEL PEAK  7(5Q33.3) WILD-TYPE    17                         1    25
D20V6, multiclass
                           clus
vv                          DEL PEAK  7(5Q33.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               3
                           clus
vv                          DEL PEAK  7(5Q33.3) WILD-TYPE
  ASIAN                                                17
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                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"
D20V7, binary
                               cls
clus                             0  1
  DEL PEAK  7(5Q33.3) MUTATED    1  3
  DEL PEAK  7(5Q33.3) WILD-TYPE 11 32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5Q33.3) MUTATED      1    3
  DEL PEAK  7(5Q33.3) WILD-TYPE   11   32
                        clus
vv                       DEL PEAK  7(5Q33.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       DEL PEAK  7(5Q33.3) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                            32
[1] 2 2
[1] FALSE

Clustering(21) Variable = DEL PEAK  8(6P21.32) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  8(6P21.32) MUTATED    5  1
  DEL PEAK  8(6P21.32) WILD-TYPE 33  8
  DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE 
                             6                             41 
  DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE 
                             1                              8 
$`DEL PEAK  8(6P21.32) MUTATED`
TCGA-FA-A4BB TCGA-FA-A7DS TCGA-GR-A4D5 TCGA-GS-A9TY TCGA-GS-A9U4 TCGA-RQ-A68N 
        4.34        23.64        42.71       109.58        12.85        25.91 

$`DEL PEAK  8(6P21.32) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34        23.28         1.91        24.62         8.15        14.04 
TCGA-FA-A86F TCGA-FF-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-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 TCGA-RQ-AAAT 
       45.14        25.15       111.58         0.03         0.56 

  DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE 
                          4.34                           0.03 
  DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE 
                        109.58                         211.23 
  DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE 
                        24.775                         31.100 
[1] "4.3 - 109.6 (24.8)" "0.0 - 211.2 (31.1)"
[1] "hr=" "1.2"
D21V2, continuous
D21V3, binary
                                cls
clus                              0  1
  DEL PEAK  8(6P21.32) MUTATED    4  2
  DEL PEAK  8(6P21.32) WILD-TYPE 22 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(6P21.32) MUTATED      4    2
  DEL PEAK  8(6P21.32) WILD-TYPE   22   19
        clus
vv       DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE
  FEMALE                            4                             22
  MALE                              2                             19
[1] 2 2
[1] FALSE
D21V4, binary
                                cls
clus                              0  1
  DEL PEAK  8(6P21.32) MUTATED    6  0
  DEL PEAK  8(6P21.32) WILD-TYPE 33  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(6P21.32) MUTATED      6    0
  DEL PEAK  8(6P21.32) WILD-TYPE   33    7
     clus
vv    DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE
  NO                             6                             33
  YES                            0                              7
[1] 2 2
[1] FALSE
                                vv
clus                             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK  8(6P21.32) MUTATED                                                                                   5
  DEL PEAK  8(6P21.32) WILD-TYPE                                                                                35
                                vv
clus                             PRIMARY DLBCL OF THE CNS
  DEL PEAK  8(6P21.32) MUTATED                          1
  DEL PEAK  8(6P21.32) WILD-TYPE                        2
                                vv
clus                             PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK  8(6P21.32) MUTATED                                    0
  DEL PEAK  8(6P21.32) WILD-TYPE                                  4
D21V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK  8(6P21.32) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                            5
  PRIMARY DLBCL OF THE CNS                                                                                     1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                           0
                                                                                   clus
vv                                                                                  DEL PEAK  8(6P21.32) 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                                                                             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
  DEL PEAK  8(6P21.32) MUTATED       1                         0     5
  DEL PEAK  8(6P21.32) WILD-TYPE    17                         1    23
D21V6, multiclass
                           clus
vv                          DEL PEAK  8(6P21.32) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                5
                           clus
vv                          DEL PEAK  8(6P21.32) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 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"
D21V7, binary
                                cls
clus                              0  1
  DEL PEAK  8(6P21.32) MUTATED    3  3
  DEL PEAK  8(6P21.32) WILD-TYPE  9 32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(6P21.32) MUTATED      3    3
  DEL PEAK  8(6P21.32) WILD-TYPE    9   32
                        clus
vv                       DEL PEAK  8(6P21.32) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                            3
                        clus
vv                       DEL PEAK  8(6P21.32) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                             32
[1] 2 2
[1] FALSE

Clustering(22) Variable = DEL PEAK  9(6Q14.1) MUTATION ANALYSIS
D22V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(6Q14.1) MUTATED   14  3
  DEL PEAK  9(6Q14.1) WILD-TYPE 24  6
  DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE 
                           17                            30 
  DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE 
                            3                             6 
$`DEL PEAK  9(6Q14.1) MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-A7CW 
       23.28        24.62        14.04        31.10        24.69        26.01 
TCGA-FF-A7CX TCGA-G8-6325 TCGA-G8-6906 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       12.66        51.98       211.23        42.71        57.17        32.28 
TCGA-GS-A9TW TCGA-GS-A9TY TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-AAAT 
       53.16       109.58        12.85        25.91         0.56 

$`DEL PEAK  9(6Q14.1) 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-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       35.54        31.73         4.14        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6907 TCGA-G8-6909 
       10.29        31.96        41.16        70.06        19.56       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GS-A9TT 
      196.60       150.51        98.07        51.98        43.86        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-RQ-A6JB 
      128.12        24.00        45.14        25.15       111.58         0.03 

  DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE 
                         0.56                          0.03 
  DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE 
                       211.23                        196.60 
  DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE 
                        26.01                         29.54 
[1] "0.6 - 211.2 (26.0)" "0.0 - 196.6 (29.5)"
[1] "hr=" "1.7"
D22V2, continuous
D22V3, binary
                               cls
clus                             0  1
  DEL PEAK  9(6Q14.1) MUTATED   10  7
  DEL PEAK  9(6Q14.1) WILD-TYPE 16 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6Q14.1) MUTATED     10    7
  DEL PEAK  9(6Q14.1) WILD-TYPE   16   14
        clus
vv       DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE
  FEMALE                          10                            16
  MALE                             7                            14
[1] 2 2
[1] FALSE
D22V4, binary
                               cls
clus                             0  1
  DEL PEAK  9(6Q14.1) MUTATED   16  1
  DEL PEAK  9(6Q14.1) WILD-TYPE 23  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6Q14.1) MUTATED     16    1
  DEL PEAK  9(6Q14.1) WILD-TYPE   23    6
     clus
vv    DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE
  NO                           16                            23
  YES                           1                             6
[1] 2 2
[1] FALSE
                               vv
clus                            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK  9(6Q14.1) MUTATED                                                                                  14
  DEL PEAK  9(6Q14.1) WILD-TYPE                                                                                26
                               vv
clus                            PRIMARY DLBCL OF THE CNS
  DEL PEAK  9(6Q14.1) MUTATED                          2
  DEL PEAK  9(6Q14.1) WILD-TYPE                        1
                               vv
clus                            PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK  9(6Q14.1) MUTATED                                    1
  DEL PEAK  9(6Q14.1) WILD-TYPE                                  3
D22V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK  9(6Q14.1) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                          14
  PRIMARY DLBCL OF THE CNS                                                                                    2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                          1
                                                                                   clus
vv                                                                                  DEL PEAK  9(6Q14.1) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                            26
  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
  DEL PEAK  9(6Q14.1) MUTATED       7                         0    10
  DEL PEAK  9(6Q14.1) WILD-TYPE    11                         1    18
D22V6, multiclass
                           clus
vv                          DEL PEAK  9(6Q14.1) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              10
                           clus
vv                          DEL PEAK  9(6Q14.1) WILD-TYPE
  ASIAN                                                11
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                               cls
clus                             0  1
  DEL PEAK  9(6Q14.1) MUTATED    6 11
  DEL PEAK  9(6Q14.1) WILD-TYPE  6 24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6Q14.1) MUTATED      6   11
  DEL PEAK  9(6Q14.1) WILD-TYPE    6   24
                        clus
vv                       DEL PEAK  9(6Q14.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          11
                        clus
vv                       DEL PEAK  9(6Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            24
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK 10(6Q22.32) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 10(6Q22.32) MUTATED   11  4
  DEL PEAK 10(6Q22.32) WILD-TYPE 27  5
  DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE 
                            15                             32 
  DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE 
                             4                              5 
$`DEL PEAK 10(6Q22.32) MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-A7CR TCGA-FF-A7CX TCGA-G8-6325 TCGA-G8-6906 
       24.62        14.04        10.29        12.66        51.98       211.23 
TCGA-G8-6909 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TY 
      116.81        42.71        57.17        32.28        38.24       109.58 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-AAAT 
       12.85        25.91         0.56 

$`DEL PEAK 10(6Q22.32) 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-A7CW TCGA-FM-8000 TCGA-G8-6324 
       27.35        22.32         9.80        26.01        31.96        41.16 
TCGA-G8-6326 TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 
       70.06        19.56       196.60       150.51        98.07        51.98 
TCGA-GR-A4D6 TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TZ 
       43.86       128.12        24.00        53.16        45.14        25.15 
TCGA-GS-A9U3 TCGA-RQ-A6JB 
      111.58         0.03 

  DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE 
                          0.56                           0.03 
  DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE 
                        211.23                         196.60 
  DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE 
                         32.28                          26.68 
[1] "0.6 - 211.2 (32.3)" "0.0 - 196.6 (26.7)"
[1] "hr=" "1.2"
D23V2, continuous
D23V3, binary
                                cls
clus                              0  1
  DEL PEAK 10(6Q22.32) MUTATED    8  7
  DEL PEAK 10(6Q22.32) WILD-TYPE 18 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.32) MUTATED      8    7
  DEL PEAK 10(6Q22.32) WILD-TYPE   18   14
        clus
vv       DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE
  FEMALE                            8                             18
  MALE                              7                             14
[1] 2 2
[1] FALSE
D23V4, binary
                                cls
clus                              0  1
  DEL PEAK 10(6Q22.32) MUTATED   14  1
  DEL PEAK 10(6Q22.32) WILD-TYPE 25  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.32) MUTATED     14    1
  DEL PEAK 10(6Q22.32) WILD-TYPE   25    6
     clus
vv    DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE
  NO                            14                             25
  YES                            1                              6
[1] 2 2
[1] FALSE
                                vv
clus                             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK 10(6Q22.32) MUTATED                                                                                  13
  DEL PEAK 10(6Q22.32) WILD-TYPE                                                                                27
                                vv
clus                             PRIMARY DLBCL OF THE CNS
  DEL PEAK 10(6Q22.32) MUTATED                          2
  DEL PEAK 10(6Q22.32) WILD-TYPE                        1
                                vv
clus                             PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK 10(6Q22.32) MUTATED                                    0
  DEL PEAK 10(6Q22.32) WILD-TYPE                                  4
D23V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK 10(6Q22.32) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                           13
  PRIMARY DLBCL OF THE CNS                                                                                     2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                           0
                                                                                   clus
vv                                                                                  DEL PEAK 10(6Q22.32) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                             27
  PRIMARY DLBCL OF THE CNS                                                                                       1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(6Q22.32) MUTATED       4                         0    11
  DEL PEAK 10(6Q22.32) WILD-TYPE    14                         1    17
D23V6, multiclass
                           clus
vv                          DEL PEAK 10(6Q22.32) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               11
                           clus
vv                          DEL PEAK 10(6Q22.32) WILD-TYPE
  ASIAN                                                 14
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                                cls
clus                              0  1
  DEL PEAK 10(6Q22.32) MUTATED    6  9
  DEL PEAK 10(6Q22.32) WILD-TYPE  6 26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.32) MUTATED      6    9
  DEL PEAK 10(6Q22.32) WILD-TYPE    6   26
                        clus
vv                       DEL PEAK 10(6Q22.32) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                            9
                        clus
vv                       DEL PEAK 10(6Q22.32) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             26
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK 11(6Q23.3) MUTATION ANALYSIS
D24V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 11(6Q23.3) MUTATED   12  3
  DEL PEAK 11(6Q23.3) WILD-TYPE 26  6
  DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE 
                           15                            32 
  DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE 
                            3                             6 
$`DEL PEAK 11(6Q23.3) MUTATED`
TCGA-FA-A82F TCGA-FF-A7CX TCGA-G8-6325 TCGA-G8-6906 TCGA-G8-6909 TCGA-GR-A4D5 
       14.04        12.66        51.98       211.23       116.81        42.71 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TW TCGA-GS-A9TY TCGA-GS-A9U4 
       57.17        32.28        38.24        53.16       109.58        12.85 
TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.91         0.03         0.56 

$`DEL PEAK 11(6Q23.3) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
        8.15        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-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-G8-6907 TCGA-G8-6914 TCGA-GR-7351 
       31.96        41.16        70.06        19.56       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TX 
       98.07        51.98        43.86       128.12        24.00        45.14 
TCGA-GS-A9TZ TCGA-GS-A9U3 
       25.15       111.58 

  DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE 
                         0.03                          1.91 
  DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE 
                       211.23                        196.60 
  DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE 
                        38.24                         25.58 
[1] "0.0 - 211.2 (38.2)" "1.9 - 196.6 (25.6)"
[1] "hr=" "1.5"
D24V2, continuous
D24V3, binary
                               cls
clus                             0  1
  DEL PEAK 11(6Q23.3) MUTATED    9  6
  DEL PEAK 11(6Q23.3) WILD-TYPE 17 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6Q23.3) MUTATED      9    6
  DEL PEAK 11(6Q23.3) WILD-TYPE   17   15
        clus
vv       DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE
  FEMALE                           9                            17
  MALE                             6                            15
[1] 2 2
[1] FALSE
D24V4, binary
                               cls
clus                             0  1
  DEL PEAK 11(6Q23.3) MUTATED   12  2
  DEL PEAK 11(6Q23.3) WILD-TYPE 27  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6Q23.3) MUTATED     12    2
  DEL PEAK 11(6Q23.3) WILD-TYPE   27    5
     clus
vv    DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE
  NO                           12                            27
  YES                           2                             5
[1] 2 2
[1] FALSE
                               vv
clus                            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK 11(6Q23.3) MUTATED                                                                                  11
  DEL PEAK 11(6Q23.3) WILD-TYPE                                                                                29
                               vv
clus                            PRIMARY DLBCL OF THE CNS
  DEL PEAK 11(6Q23.3) MUTATED                          3
  DEL PEAK 11(6Q23.3) WILD-TYPE                        0
                               vv
clus                            PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK 11(6Q23.3) MUTATED                                    1
  DEL PEAK 11(6Q23.3) WILD-TYPE                                  3
D24V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK 11(6Q23.3) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                          11
  PRIMARY DLBCL OF THE CNS                                                                                    3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                          1
                                                                                   clus
vv                                                                                  DEL PEAK 11(6Q23.3) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                            29
  PRIMARY DLBCL OF THE CNS                                                                                      0
  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
  DEL PEAK 11(6Q23.3) MUTATED       2                         0    13
  DEL PEAK 11(6Q23.3) WILD-TYPE    16                         1    15
D24V6, multiclass
                           clus
vv                          DEL PEAK 11(6Q23.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              13
                           clus
vv                          DEL PEAK 11(6Q23.3) WILD-TYPE
  ASIAN                                                16
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                               cls
clus                             0  1
  DEL PEAK 11(6Q23.3) MUTATED    7  8
  DEL PEAK 11(6Q23.3) WILD-TYPE  5 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6Q23.3) MUTATED      7    8
  DEL PEAK 11(6Q23.3) WILD-TYPE    5   27
                        clus
vv                       DEL PEAK 11(6Q23.3) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                           8
                        clus
vv                       DEL PEAK 11(6Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            27
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK 12(7Q33) MUTATION ANALYSIS
D25V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 12(7Q33) MUTATED    4  1
  DEL PEAK 12(7Q33) WILD-TYPE 34  8
  DEL PEAK 12(7Q33) MUTATED DEL PEAK 12(7Q33) WILD-TYPE 
                          5                          42 
  DEL PEAK 12(7Q33) MUTATED DEL PEAK 12(7Q33) WILD-TYPE 
                          1                           8 
$`DEL PEAK 12(7Q33) MUTATED`
TCGA-GR-7353 TCGA-GS-A9TQ TCGA-GS-A9TW TCGA-GS-A9U4 TCGA-RQ-AAAT 
       98.07        32.28        53.16        12.85         0.56 

$`DEL PEAK 12(7Q33) 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-A4D4 
      211.23        19.56       116.81       196.60       150.51        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-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-RQ-A68N TCGA-RQ-A6JB 
       45.14       109.58        25.15       111.58        25.91         0.03 

  DEL PEAK 12(7Q33) MUTATED DEL PEAK 12(7Q33) WILD-TYPE 
                       0.56                        0.03 
  DEL PEAK 12(7Q33) MUTATED DEL PEAK 12(7Q33) WILD-TYPE 
                      98.07                      211.23 
  DEL PEAK 12(7Q33) MUTATED DEL PEAK 12(7Q33) WILD-TYPE 
                      32.28                       26.68 
[1] "0.6 - 98.1 (32.3)"  "0.0 - 211.2 (26.7)"
[1] "hr=" "1.5"
D25V2, continuous
D25V3, binary
                             cls
clus                           0  1
  DEL PEAK 12(7Q33) MUTATED    4  1
  DEL PEAK 12(7Q33) WILD-TYPE 22 20
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(7Q33) MUTATED      4    1
  DEL PEAK 12(7Q33) WILD-TYPE   22   20
        clus
vv       DEL PEAK 12(7Q33) MUTATED DEL PEAK 12(7Q33) WILD-TYPE
  FEMALE                         4                          22
  MALE                           1                          20
[1] 2 2
[1] FALSE
D25V4, binary
                             cls
clus                           0  1
  DEL PEAK 12(7Q33) MUTATED    4  1
  DEL PEAK 12(7Q33) WILD-TYPE 35  6
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(7Q33) MUTATED      4    1
  DEL PEAK 12(7Q33) WILD-TYPE   35    6
     clus
vv    DEL PEAK 12(7Q33) MUTATED DEL PEAK 12(7Q33) WILD-TYPE
  NO                          4                          35
  YES                         1                           6
[1] 2 2
[1] FALSE
                             vv
clus                          DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK 12(7Q33) MUTATED                                                                                   3
  DEL PEAK 12(7Q33) WILD-TYPE                                                                                37
                             vv
clus                          PRIMARY DLBCL OF THE CNS
  DEL PEAK 12(7Q33) MUTATED                          1
  DEL PEAK 12(7Q33) WILD-TYPE                        2
                             vv
clus                          PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK 12(7Q33) MUTATED                                    1
  DEL PEAK 12(7Q33) WILD-TYPE                                  3
D25V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK 12(7Q33) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                         3
  PRIMARY DLBCL OF THE CNS                                                                                  1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                        1
                                                                                   clus
vv                                                                                  DEL PEAK 12(7Q33) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                          37
  PRIMARY DLBCL OF THE CNS                                                                                    2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                          3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(7Q33) MUTATED       0                         0     5
  DEL PEAK 12(7Q33) WILD-TYPE    18                         1    23
D25V6, multiclass
                           clus
vv                          DEL PEAK 12(7Q33) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                             5
                           clus
vv                          DEL PEAK 12(7Q33) WILD-TYPE
  ASIAN                                              18
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              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"
D25V7, binary
                             cls
clus                           0  1
  DEL PEAK 12(7Q33) MUTATED    4  1
  DEL PEAK 12(7Q33) WILD-TYPE  8 34
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(7Q33) MUTATED      4    1
  DEL PEAK 12(7Q33) WILD-TYPE    8   34
                        clus
vv                       DEL PEAK 12(7Q33) MUTATED DEL PEAK 12(7Q33) WILD-TYPE
  HISPANIC OR LATINO                             4                           8
  NOT HISPANIC OR LATINO                         1                          34
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK 13(8P23.2) MUTATION ANALYSIS
D26V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 13(8P23.2) MUTATED   10  1
  DEL PEAK 13(8P23.2) WILD-TYPE 28  8
  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                           11                            36 
  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                            1                             8 
$`DEL PEAK 13(8P23.2) MUTATED`
TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8047 TCGA-GR-A4D6 
       24.62         8.15        14.04        18.18         4.14        43.86 
TCGA-GS-A9TQ TCGA-GS-A9TW TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-RQ-A68N 
       32.28        53.16       109.58        25.15        25.91 

$`DEL PEAK 13(8P23.2) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FF-8041 
        4.34         4.34        23.28         1.91        23.64        35.54 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       31.10        31.73        24.69        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
       10.29        26.01        12.66        31.96        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       70.06       211.23        19.56       116.81       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU 
       98.07        51.98        42.71        57.17        38.24       128.12 
TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB TCGA-RQ-AAAT 
       24.00        45.14       111.58        12.85         0.03         0.56 

  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                         4.14                          0.03 
  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                       109.58                        211.23 
  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                       25.150                        31.415 
[1] "4.1 - 109.6 (25.1)" "0.0 - 211.2 (31.4)"
[1] "hr=" "1.7"
D26V2, continuous
D26V3, binary
                               cls
clus                             0  1
  DEL PEAK 13(8P23.2) MUTATED    9  2
  DEL PEAK 13(8P23.2) WILD-TYPE 17 19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.2) MUTATED      9    2
  DEL PEAK 13(8P23.2) WILD-TYPE   17   19
        clus
vv       DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE
  FEMALE                           9                            17
  MALE                             2                            19
[1] 2 2
[1] FALSE
D26V4, binary
                               cls
clus                             0  1
  DEL PEAK 13(8P23.2) MUTATED    9  2
  DEL PEAK 13(8P23.2) WILD-TYPE 30  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.2) MUTATED      9    2
  DEL PEAK 13(8P23.2) WILD-TYPE   30    5
     clus
vv    DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE
  NO                            9                            30
  YES                           2                             5
[1] 2 2
[1] FALSE
                               vv
clus                            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK 13(8P23.2) MUTATED                                                                                   8
  DEL PEAK 13(8P23.2) WILD-TYPE                                                                                32
                               vv
clus                            PRIMARY DLBCL OF THE CNS
  DEL PEAK 13(8P23.2) MUTATED                          1
  DEL PEAK 13(8P23.2) WILD-TYPE                        2
                               vv
clus                            PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK 13(8P23.2) MUTATED                                    2
  DEL PEAK 13(8P23.2) WILD-TYPE                                  2
D26V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK 13(8P23.2) 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                                                                          2
                                                                                   clus
vv                                                                                  DEL PEAK 13(8P23.2) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                            32
  PRIMARY DLBCL OF THE CNS                                                                                      2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                            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
  DEL PEAK 13(8P23.2) MUTATED       5                         0     6
  DEL PEAK 13(8P23.2) WILD-TYPE    13                         1    22
D26V6, multiclass
                           clus
vv                          DEL PEAK 13(8P23.2) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               6
                           clus
vv                          DEL PEAK 13(8P23.2) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                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"
D26V7, binary
                               cls
clus                             0  1
  DEL PEAK 13(8P23.2) MUTATED    5  6
  DEL PEAK 13(8P23.2) WILD-TYPE  7 29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.2) MUTATED      5    6
  DEL PEAK 13(8P23.2) WILD-TYPE    7   29
                        clus
vv                       DEL PEAK 13(8P23.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                           6
                        clus
vv                       DEL PEAK 13(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            29
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK 14(8Q12.1) MUTATION ANALYSIS
D27V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 14(8Q12.1) MUTATED    8  1
  DEL PEAK 14(8Q12.1) WILD-TYPE 30  8
  DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE 
                            9                            38 
  DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE 
                            1                             8 
$`DEL PEAK 14(8Q12.1) MUTATED`
TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A86F TCGA-FF-8047 TCGA-FF-A7CR TCGA-GR-7353 
       24.62        23.64        18.18         4.14        10.29        98.07 
TCGA-GS-A9TQ TCGA-GS-A9TY TCGA-RQ-A68N 
       32.28       109.58        25.91 

$`DEL PEAK 14(8Q12.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34         4.34        23.28         1.91         8.15        14.04 
TCGA-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-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
        9.80        26.01        12.66        31.96        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       70.06       211.23        19.56       116.81       196.60       150.51 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TU 
       51.98        42.71        43.86        57.17        38.24       128.12 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 
       24.00        53.16        45.14        25.15       111.58        12.85 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE 
                         4.14                          0.03 
  DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE 
                       109.58                        211.23 
  DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE 
                       24.620                        31.415 
[1] "4.1 - 109.6 (24.6)" "0.0 - 211.2 (31.4)"
[1] "hr=" "1.3"
D27V2, continuous
D27V3, binary
                               cls
clus                             0  1
  DEL PEAK 14(8Q12.1) MUTATED    6  3
  DEL PEAK 14(8Q12.1) WILD-TYPE 20 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8Q12.1) MUTATED      6    3
  DEL PEAK 14(8Q12.1) WILD-TYPE   20   18
        clus
vv       DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE
  FEMALE                           6                            20
  MALE                             3                            18
[1] 2 2
[1] FALSE
D27V4, binary
                               cls
clus                             0  1
  DEL PEAK 14(8Q12.1) MUTATED    9  0
  DEL PEAK 14(8Q12.1) WILD-TYPE 30  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8Q12.1) MUTATED      9    0
  DEL PEAK 14(8Q12.1) WILD-TYPE   30    7
     clus
vv    DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE
  NO                            9                            30
  YES                           0                             7
[1] 2 2
[1] FALSE
                               vv
clus                            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK 14(8Q12.1) MUTATED                                                                                   8
  DEL PEAK 14(8Q12.1) WILD-TYPE                                                                                32
                               vv
clus                            PRIMARY DLBCL OF THE CNS
  DEL PEAK 14(8Q12.1) MUTATED                          1
  DEL PEAK 14(8Q12.1) WILD-TYPE                        2
                               vv
clus                            PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK 14(8Q12.1) MUTATED                                    0
  DEL PEAK 14(8Q12.1) WILD-TYPE                                  4
D27V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK 14(8Q12.1) 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                                                                          0
                                                                                   clus
vv                                                                                  DEL PEAK 14(8Q12.1) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                            32
  PRIMARY DLBCL OF THE CNS                                                                                      2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                            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
  DEL PEAK 14(8Q12.1) MUTATED       4                         0     5
  DEL PEAK 14(8Q12.1) WILD-TYPE    14                         1    23
D27V6, multiclass
                           clus
vv                          DEL PEAK 14(8Q12.1) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               5
                           clus
vv                          DEL PEAK 14(8Q12.1) WILD-TYPE
  ASIAN                                                14
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                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"
D27V7, binary
                               cls
clus                             0  1
  DEL PEAK 14(8Q12.1) MUTATED    3  6
  DEL PEAK 14(8Q12.1) WILD-TYPE  9 29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8Q12.1) MUTATED      3    6
  DEL PEAK 14(8Q12.1) WILD-TYPE    9   29
                        clus
vv                       DEL PEAK 14(8Q12.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                           6
                        clus
vv                       DEL PEAK 14(8Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                            29
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK 15(9P21.3) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 15(9P21.3) MUTATED   13  4
  DEL PEAK 15(9P21.3) WILD-TYPE 25  5
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                           17                            30 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                            4                             5 
$`DEL PEAK 15(9P21.3) MUTATED`
TCGA-FA-A4XK TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FF-8042 TCGA-FF-8047 TCGA-FF-A7CQ 
       23.28        23.64         8.15        31.10         4.14         9.80 
TCGA-FF-A7CR TCGA-FF-A7CW TCGA-G8-6325 TCGA-G8-6906 TCGA-GR-A4D6 TCGA-GR-A4D9 
       10.29        26.01        51.98       211.23        43.86        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-RQ-A68N TCGA-RQ-A6JB 
       32.28        38.24       128.12        25.91         0.03 

$`DEL PEAK 15(9P21.3) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A82F TCGA-FA-A86F 
        4.34         4.34         1.91        24.62        14.04        18.18 
TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CX 
       35.54        31.73        24.69        27.35        22.32        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       31.96        41.16        70.06        19.56       116.81       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GS-A9TV TCGA-GS-A9TW 
      150.51        98.07        51.98        42.71        24.00        53.16 
TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-AAAT 
       45.14       109.58        25.15       111.58        12.85         0.56 

  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                         0.03                          0.56 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                       211.23                        196.60 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                        26.01                         29.54 
[1] "0.0 - 211.2 (26.0)" "0.6 - 196.6 (29.5)"
[1] "hr=" "1.1"
D28V2, continuous
D28V3, binary
                               cls
clus                             0  1
  DEL PEAK 15(9P21.3) MUTATED    8  9
  DEL PEAK 15(9P21.3) WILD-TYPE 18 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED      8    9
  DEL PEAK 15(9P21.3) WILD-TYPE   18   12
        clus
vv       DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  FEMALE                           8                            18
  MALE                             9                            12
[1] 2 2
[1] FALSE
D28V4, binary
                               cls
clus                             0  1
  DEL PEAK 15(9P21.3) MUTATED   14  2
  DEL PEAK 15(9P21.3) WILD-TYPE 25  5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED     14    2
  DEL PEAK 15(9P21.3) WILD-TYPE   25    5
     clus
vv    DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  NO                           14                            25
  YES                           2                             5
[1] 2 2
[1] FALSE
                               vv
clus                            DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK 15(9P21.3) MUTATED                                                                                  15
  DEL PEAK 15(9P21.3) WILD-TYPE                                                                                25
                               vv
clus                            PRIMARY DLBCL OF THE CNS
  DEL PEAK 15(9P21.3) MUTATED                          2
  DEL PEAK 15(9P21.3) WILD-TYPE                        1
                               vv
clus                            PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK 15(9P21.3) MUTATED                                    0
  DEL PEAK 15(9P21.3) WILD-TYPE                                  4
D28V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK 15(9P21.3) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                          15
  PRIMARY DLBCL OF THE CNS                                                                                    2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                          0
                                                                                   clus
vv                                                                                  DEL PEAK 15(9P21.3) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                            25
  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
  DEL PEAK 15(9P21.3) MUTATED       9                         0     8
  DEL PEAK 15(9P21.3) WILD-TYPE     9                         1    20
D28V6, multiclass
                           clus
vv                          DEL PEAK 15(9P21.3) MUTATED
  ASIAN                                               9
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               8
                           clus
vv                          DEL PEAK 15(9P21.3) WILD-TYPE
  ASIAN                                                 9
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                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"
D28V7, binary
                               cls
clus                             0  1
  DEL PEAK 15(9P21.3) MUTATED    4 13
  DEL PEAK 15(9P21.3) WILD-TYPE  8 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED      4   13
  DEL PEAK 15(9P21.3) WILD-TYPE    8   22
                        clus
vv                       DEL PEAK 15(9P21.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          13
                        clus
vv                       DEL PEAK 15(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                            22
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK 16(10Q23.31) MUTATION ANALYSIS
D29V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 16(10Q23.31) MUTATED    6  2
  DEL PEAK 16(10Q23.31) WILD-TYPE 32  7
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                              8                              39 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                              2                               7 
$`DEL PEAK 16(10Q23.31) MUTATED`
TCGA-FA-A7Q1 TCGA-G8-6907 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GS-A9TW 
        8.15        19.56        98.07        51.98        43.86        53.16 
TCGA-GS-A9TY TCGA-RQ-A6JB 
      109.58         0.03 

$`DEL PEAK 16(10Q23.31) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       12.66        31.96        41.16        51.98        70.06       211.23 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TQ 
      116.81       196.60       150.51        42.71        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 
       38.24       128.12        24.00        45.14        25.15       111.58 
TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-AAAT 
       12.85        25.91         0.56 

  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                           0.03                            0.56 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                         109.58                          211.23 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                          47.92                           26.01 
[1] "0.0 - 109.6 (47.9)" "0.6 - 211.2 (26.0)"
[1] "hr=" "1.8"
D29V2, continuous
D29V3, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED    7  1
  DEL PEAK 16(10Q23.31) WILD-TYPE 19 20
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED      7    1
  DEL PEAK 16(10Q23.31) WILD-TYPE   19   20
        clus
vv       DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  FEMALE                             7                              19
  MALE                               1                              20
[1] 2 2
[1] FALSE
D29V4, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED    6  1
  DEL PEAK 16(10Q23.31) WILD-TYPE 33  6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED      6    1
  DEL PEAK 16(10Q23.31) WILD-TYPE   33    6
     clus
vv    DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  NO                              6                              33
  YES                             1                               6
[1] 2 2
[1] FALSE
                                 vv
clus                              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK 16(10Q23.31) MUTATED                                                                                   6
  DEL PEAK 16(10Q23.31) WILD-TYPE                                                                                34
                                 vv
clus                              PRIMARY DLBCL OF THE CNS
  DEL PEAK 16(10Q23.31) MUTATED                          1
  DEL PEAK 16(10Q23.31) WILD-TYPE                        2
                                 vv
clus                              PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK 16(10Q23.31) MUTATED                                    1
  DEL PEAK 16(10Q23.31) WILD-TYPE                                  3
D29V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK 16(10Q23.31) 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                                                                                  DEL PEAK 16(10Q23.31) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                              34
  PRIMARY DLBCL OF THE CNS                                                                                        2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(10Q23.31) MUTATED       2                         0     6
  DEL PEAK 16(10Q23.31) WILD-TYPE    16                         1    22
D29V6, multiclass
                           clus
vv                          DEL PEAK 16(10Q23.31) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                 6
                           clus
vv                          DEL PEAK 16(10Q23.31) WILD-TYPE
  ASIAN                                                  16
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  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"
D29V7, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED    2  6
  DEL PEAK 16(10Q23.31) WILD-TYPE 10 29
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED      2    6
  DEL PEAK 16(10Q23.31) WILD-TYPE   10   29
                        clus
vv                       DEL PEAK 16(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                             6
                        clus
vv                       DEL PEAK 16(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                  10
  NOT HISPANIC OR LATINO                              29
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK 17(12P13.2) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 17(12P13.2) MUTATED    8  0
  DEL PEAK 17(12P13.2) WILD-TYPE 30  9
  DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE 
                             8                             39 
  DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE 
                             0                              9 
$`DEL PEAK 17(12P13.2) MUTATED`
TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FF-8043 TCGA-FF-A7CQ TCGA-GR-A4D4 TCGA-GR-A4D6 
       24.62        23.64        31.73         9.80        51.98        43.86 
TCGA-GS-A9TY TCGA-RQ-A68N 
      109.58        25.91 

$`DEL PEAK 17(12P13.2) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34         4.34        23.28         1.91         8.15        14.04 
TCGA-FA-A86F TCGA-FF-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-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
       22.32        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-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT 
      150.51        98.07        42.71        57.17        32.28        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 
      128.12        24.00        53.16        45.14        25.15       111.58 
TCGA-GS-A9U4 TCGA-RQ-A6JB TCGA-RQ-AAAT 
       12.85         0.03         0.56 

  DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE 
                          9.80                           0.03 
  DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE 
                        109.58                         211.23 
  DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE 
                         28.82                          27.35 
[1] "9.8 - 109.6 (28.8)" "0.0 - 211.2 (27.4)"
[1] "hr="     "2.5e+08"
D30V2, continuous
D30V3, binary
                                cls
clus                              0  1
  DEL PEAK 17(12P13.2) MUTATED    6  2
  DEL PEAK 17(12P13.2) WILD-TYPE 20 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(12P13.2) MUTATED      6    2
  DEL PEAK 17(12P13.2) WILD-TYPE   20   19
        clus
vv       DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE
  FEMALE                            6                             20
  MALE                              2                             19
[1] 2 2
[1] FALSE
D30V4, binary
                                cls
clus                              0  1
  DEL PEAK 17(12P13.2) MUTATED    8  0
  DEL PEAK 17(12P13.2) WILD-TYPE 31  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(12P13.2) MUTATED      8    0
  DEL PEAK 17(12P13.2) WILD-TYPE   31    7
     clus
vv    DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE
  NO                             8                             31
  YES                            0                              7
[1] 2 2
[1] FALSE
                                vv
clus                             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK 17(12P13.2) MUTATED                                                                                   7
  DEL PEAK 17(12P13.2) WILD-TYPE                                                                                33
                                vv
clus                             PRIMARY DLBCL OF THE CNS
  DEL PEAK 17(12P13.2) MUTATED                          1
  DEL PEAK 17(12P13.2) WILD-TYPE                        2
                                vv
clus                             PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK 17(12P13.2) MUTATED                                    0
  DEL PEAK 17(12P13.2) WILD-TYPE                                  4
D30V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK 17(12P13.2) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                            7
  PRIMARY DLBCL OF THE CNS                                                                                     1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                           0
                                                                                   clus
vv                                                                                  DEL PEAK 17(12P13.2) 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                                                                             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
  DEL PEAK 17(12P13.2) MUTATED       5                         0     3
  DEL PEAK 17(12P13.2) WILD-TYPE    13                         1    25
D30V6, multiclass
                           clus
vv                          DEL PEAK 17(12P13.2) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                3
                           clus
vv                          DEL PEAK 17(12P13.2) WILD-TYPE
  ASIAN                                                 13
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 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"
D30V7, binary
                                cls
clus                              0  1
  DEL PEAK 17(12P13.2) MUTATED    2  6
  DEL PEAK 17(12P13.2) WILD-TYPE 10 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(12P13.2) MUTATED      2    6
  DEL PEAK 17(12P13.2) WILD-TYPE   10   29
                        clus
vv                       DEL PEAK 17(12P13.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       DEL PEAK 17(12P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                             29
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK 18(13Q14.2) MUTATION ANALYSIS
D31V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(13Q14.2) MUTATED    5  1
  DEL PEAK 18(13Q14.2) WILD-TYPE 33  8
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                             6                             41 
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                             1                              8 
$`DEL PEAK 18(13Q14.2) MUTATED`
TCGA-FF-8043 TCGA-G8-6907 TCGA-GR-A4D4 TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-RQ-AAAT 
       31.73        19.56        51.98       109.58        25.15         0.56 

$`DEL PEAK 18(13Q14.2) 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-8046 
        8.15        14.04        18.18        35.54        31.10        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-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 
      116.81       196.60       150.51        98.07        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       57.17        32.28        38.24       128.12        24.00        53.16 
TCGA-GS-A9TX TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
       45.14       111.58        12.85        25.91         0.03 

  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                          0.56                           0.03 
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                        109.58                         211.23 
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                         28.44                          27.35 
[1] "0.6 - 109.6 (28.4)" "0.0 - 211.2 (27.4)"
[1] "hr=" "1.2"
D31V2, continuous
D31V3, binary
                                cls
clus                              0  1
  DEL PEAK 18(13Q14.2) MUTATED    5  1
  DEL PEAK 18(13Q14.2) WILD-TYPE 21 20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(13Q14.2) MUTATED      5    1
  DEL PEAK 18(13Q14.2) WILD-TYPE   21   20
        clus
vv       DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE
  FEMALE                            5                             21
  MALE                              1                             20
[1] 2 2
[1] FALSE
D31V4, binary
                                cls
clus                              0  1
  DEL PEAK 18(13Q14.2) MUTATED    5  1
  DEL PEAK 18(13Q14.2) WILD-TYPE 34  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(13Q14.2) MUTATED      5    1
  DEL PEAK 18(13Q14.2) WILD-TYPE   34    6
     clus
vv    DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE
  NO                             5                             34
  YES                            1                              6
[1] 2 2
[1] FALSE
                                vv
clus                             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK 18(13Q14.2) MUTATED                                                                                   4
  DEL PEAK 18(13Q14.2) WILD-TYPE                                                                                36
                                vv
clus                             PRIMARY DLBCL OF THE CNS
  DEL PEAK 18(13Q14.2) MUTATED                          1
  DEL PEAK 18(13Q14.2) WILD-TYPE                        2
                                vv
clus                             PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK 18(13Q14.2) MUTATED                                    1
  DEL PEAK 18(13Q14.2) WILD-TYPE                                  3
D31V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK 18(13Q14.2) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                            4
  PRIMARY DLBCL OF THE CNS                                                                                     1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                           1
                                                                                   clus
vv                                                                                  DEL PEAK 18(13Q14.2) 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
  DEL PEAK 18(13Q14.2) MUTATED       1                         0     5
  DEL PEAK 18(13Q14.2) WILD-TYPE    17                         1    23
D31V6, multiclass
                           clus
vv                          DEL PEAK 18(13Q14.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                5
                           clus
vv                          DEL PEAK 18(13Q14.2) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 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"
D31V7, binary
                                cls
clus                              0  1
  DEL PEAK 18(13Q14.2) MUTATED    3  3
  DEL PEAK 18(13Q14.2) WILD-TYPE  9 32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(13Q14.2) MUTATED      3    3
  DEL PEAK 18(13Q14.2) WILD-TYPE    9   32
                        clus
vv                       DEL PEAK 18(13Q14.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                            3
                        clus
vv                       DEL PEAK 18(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                             32
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK 19(15Q21.1) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 19(15Q21.1) MUTATED   12  1
  DEL PEAK 19(15Q21.1) WILD-TYPE 26  8
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                            13                             34 
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                             1                              8 
$`DEL PEAK 19(15Q21.1) MUTATED`
TCGA-FA-8693 TCGA-FA-A6HO TCGA-FA-A86F TCGA-FF-8043 TCGA-G8-6907 TCGA-GR-7351 
        4.34        24.62        18.18        31.73        19.56       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TW 
       98.07        51.98        43.86        32.28        38.24        53.16 
TCGA-RQ-A6JB 
        0.03 

$`DEL PEAK 19(15Q21.1) WILD-TYPE`
TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34        23.28         1.91        23.64         8.15        14.04 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.10        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66        31.96        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-A4D5 
       51.98        70.06       211.23       116.81       196.60        42.71 
TCGA-GR-A4D9 TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ 
       57.17       128.12        24.00        45.14       109.58        25.15 
TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-AAAT 
      111.58        12.85        25.91         0.56 

  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                          0.03                           0.56 
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                        150.51                         211.23 
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                         32.28                          25.96 
[1] "0.0 - 150.5 (32.3)" "0.6 - 211.2 (26.0)"
[1] "hr=" "2.6"
D32V2, continuous
D32V3, binary
                                cls
clus                              0  1
  DEL PEAK 19(15Q21.1) MUTATED   10  3
  DEL PEAK 19(15Q21.1) WILD-TYPE 16 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(15Q21.1) MUTATED     10    3
  DEL PEAK 19(15Q21.1) WILD-TYPE   16   18
        clus
vv       DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE
  FEMALE                           10                             16
  MALE                              3                             18
[1] 2 2
[1] FALSE
D32V4, binary
                                cls
clus                              0  1
  DEL PEAK 19(15Q21.1) MUTATED    9  3
  DEL PEAK 19(15Q21.1) WILD-TYPE 30  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(15Q21.1) MUTATED      9    3
  DEL PEAK 19(15Q21.1) WILD-TYPE   30    4
     clus
vv    DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE
  NO                             9                             30
  YES                            3                              4
[1] 2 2
[1] FALSE
                                vv
clus                             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK 19(15Q21.1) MUTATED                                                                                  11
  DEL PEAK 19(15Q21.1) WILD-TYPE                                                                                29
                                vv
clus                             PRIMARY DLBCL OF THE CNS
  DEL PEAK 19(15Q21.1) MUTATED                          1
  DEL PEAK 19(15Q21.1) WILD-TYPE                        2
                                vv
clus                             PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK 19(15Q21.1) MUTATED                                    1
  DEL PEAK 19(15Q21.1) WILD-TYPE                                  3
D32V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK 19(15Q21.1) 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                                                                                  DEL PEAK 19(15Q21.1) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                             29
  PRIMARY DLBCL OF THE CNS                                                                                       2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(15Q21.1) MUTATED       3                         0    10
  DEL PEAK 19(15Q21.1) WILD-TYPE    15                         1    18
D32V6, multiclass
                           clus
vv                          DEL PEAK 19(15Q21.1) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               10
                           clus
vv                          DEL PEAK 19(15Q21.1) WILD-TYPE
  ASIAN                                                 15
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                                cls
clus                              0  1
  DEL PEAK 19(15Q21.1) MUTATED    3 10
  DEL PEAK 19(15Q21.1) WILD-TYPE  9 25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(15Q21.1) MUTATED      3   10
  DEL PEAK 19(15Q21.1) WILD-TYPE    9   25
                        clus
vv                       DEL PEAK 19(15Q21.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           10
                        clus
vv                       DEL PEAK 19(15Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                             25
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK 20(16P13.13) MUTATION ANALYSIS
D33V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 20(16P13.13) MUTATED    5  0
  DEL PEAK 20(16P13.13) WILD-TYPE 33  9
  DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE 
                              5                              42 
  DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE 
                              0                               9 
$`DEL PEAK 20(16P13.13) MUTATED`
TCGA-FA-A6HO TCGA-FF-8041 TCGA-FF-8043 TCGA-FM-8000 TCGA-GS-A9TZ 
       24.62        35.54        31.73        31.96        25.15 

$`DEL PEAK 20(16P13.13) 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-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       14.04        18.18        31.10        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-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-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-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
      109.58       111.58        12.85        25.91         0.03         0.56 

  DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE 
                          24.62                            0.03 
  DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE 
                          35.54                          211.23 
  DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE 
                          31.73                           26.68 
[1] "24.6 - 35.5 (31.7)" "0.0 - 211.2 (26.7)"
[1] "hr="     "8.3e+07"
D33V2, continuous
D33V3, binary
                                 cls
clus                               0  1
  DEL PEAK 20(16P13.13) MUTATED    4  1
  DEL PEAK 20(16P13.13) WILD-TYPE 22 20
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(16P13.13) MUTATED      4    1
  DEL PEAK 20(16P13.13) WILD-TYPE   22   20
        clus
vv       DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE
  FEMALE                             4                              22
  MALE                               1                              20
[1] 2 2
[1] FALSE
D33V4, binary
                                 cls
clus                               0  1
  DEL PEAK 20(16P13.13) MUTATED    4  1
  DEL PEAK 20(16P13.13) WILD-TYPE 35  6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(16P13.13) MUTATED      4    1
  DEL PEAK 20(16P13.13) WILD-TYPE   35    6
     clus
vv    DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE
  NO                              4                              35
  YES                             1                               6
[1] 2 2
[1] FALSE
                                 vv
clus                              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK 20(16P13.13) MUTATED                                                                                   3
  DEL PEAK 20(16P13.13) WILD-TYPE                                                                                37
                                 vv
clus                              PRIMARY DLBCL OF THE CNS
  DEL PEAK 20(16P13.13) MUTATED                          0
  DEL PEAK 20(16P13.13) WILD-TYPE                        3
                                 vv
clus                              PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK 20(16P13.13) MUTATED                                    2
  DEL PEAK 20(16P13.13) WILD-TYPE                                  2
D33V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK 20(16P13.13) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                             3
  PRIMARY DLBCL OF THE CNS                                                                                      0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                            2
                                                                                   clus
vv                                                                                  DEL PEAK 20(16P13.13) 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
  DEL PEAK 20(16P13.13) MUTATED       3                         0     2
  DEL PEAK 20(16P13.13) WILD-TYPE    15                         1    26
D33V6, multiclass
                           clus
vv                          DEL PEAK 20(16P13.13) MUTATED
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                 2
                           clus
vv                          DEL PEAK 20(16P13.13) WILD-TYPE
  ASIAN                                                  15
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  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"
D33V7, binary
                                 cls
clus                               0  1
  DEL PEAK 20(16P13.13) MUTATED    1  4
  DEL PEAK 20(16P13.13) WILD-TYPE 11 31
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(16P13.13) MUTATED      1    4
  DEL PEAK 20(16P13.13) WILD-TYPE   11   31
                        clus
vv                       DEL PEAK 20(16P13.13) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                             4
                        clus
vv                       DEL PEAK 20(16P13.13) WILD-TYPE
  HISPANIC OR LATINO                                  11
  NOT HISPANIC OR LATINO                              31
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK 21(16Q23.1) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 21(16Q23.1) MUTATED    4  1
  DEL PEAK 21(16Q23.1) WILD-TYPE 34  8
  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                             5                             42 
  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                             1                              8 
$`DEL PEAK 21(16Q23.1) MUTATED`
TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8043 TCGA-FF-8047 TCGA-GR-A4D4 
        1.91        24.62        31.73         4.14        51.98 

$`DEL PEAK 21(16Q23.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34         4.34        23.28        23.64         8.15        14.04 
TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 
       18.18        35.54        31.10        24.69        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66        31.96        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        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-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 

  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                          1.91                           0.03 
  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                         51.98                         211.23 
  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                        24.620                         29.225 
[1] "1.9 - 52.0 (24.6)"  "0.0 - 211.2 (29.2)"
[1] "hr=" "1.8"
D34V2, continuous
D34V3, binary
                                cls
clus                              0  1
  DEL PEAK 21(16Q23.1) MUTATED    4  1
  DEL PEAK 21(16Q23.1) WILD-TYPE 22 20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(16Q23.1) MUTATED      4    1
  DEL PEAK 21(16Q23.1) WILD-TYPE   22   20
        clus
vv       DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE
  FEMALE                            4                             22
  MALE                              1                             20
[1] 2 2
[1] FALSE
D34V4, binary
                                cls
clus                              0  1
  DEL PEAK 21(16Q23.1) MUTATED    5  0
  DEL PEAK 21(16Q23.1) WILD-TYPE 34  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(16Q23.1) MUTATED      5    0
  DEL PEAK 21(16Q23.1) WILD-TYPE   34    7
     clus
vv    DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE
  NO                             5                             34
  YES                            0                              7
[1] 2 2
[1] FALSE
                                vv
clus                             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK 21(16Q23.1) MUTATED                                                                                   5
  DEL PEAK 21(16Q23.1) WILD-TYPE                                                                                35
                                vv
clus                             PRIMARY DLBCL OF THE CNS
  DEL PEAK 21(16Q23.1) MUTATED                          0
  DEL PEAK 21(16Q23.1) WILD-TYPE                        3
                                vv
clus                             PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK 21(16Q23.1) MUTATED                                    0
  DEL PEAK 21(16Q23.1) WILD-TYPE                                  4
D34V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK 21(16Q23.1) 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                                                                                  DEL PEAK 21(16Q23.1) 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
  DEL PEAK 21(16Q23.1) MUTATED       4                         0     1
  DEL PEAK 21(16Q23.1) WILD-TYPE    14                         1    27
D34V6, multiclass
                           clus
vv                          DEL PEAK 21(16Q23.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                1
                           clus
vv                          DEL PEAK 21(16Q23.1) WILD-TYPE
  ASIAN                                                 14
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 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"
D34V7, binary
                                cls
clus                              0  1
  DEL PEAK 21(16Q23.1) MUTATED    0  5
  DEL PEAK 21(16Q23.1) WILD-TYPE 12 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(16Q23.1) MUTATED      0    5
  DEL PEAK 21(16Q23.1) WILD-TYPE   12   30
                        clus
vv                       DEL PEAK 21(16Q23.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            5
                        clus
vv                       DEL PEAK 21(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                             30
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 22(17P13.1) MUTATION ANALYSIS
D35V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 22(17P13.1) MUTATED   12  0
  DEL PEAK 22(17P13.1) WILD-TYPE 26  9
  DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE 
                            12                             35 
  DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE 
                             0                              9 
$`DEL PEAK 22(17P13.1) MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8043 TCGA-FF-8047 TCGA-GR-A4D4 TCGA-GS-A9TQ 
       24.62        14.04        31.73         4.14        51.98        32.28 
TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-RQ-A68N TCGA-RQ-AAAT 
       53.16        45.14       109.58        25.15        25.91         0.56 

$`DEL PEAK 22(17P13.1) 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-8061 TCGA-FF-8062 
       18.18        35.54        31.10        24.69        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66        31.96        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
       51.98        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-A9TT 
      150.51        98.07        42.71        43.86        57.17        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB 
      128.12        24.00       111.58        12.85         0.03 

  DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE 
                          0.56                           0.03 
  DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE 
                        109.58                         211.23 
  DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE 
                         28.82                          27.35 
[1] "0.6 - 109.6 (28.8)" "0.0 - 211.2 (27.4)"
[1] "hr="     "2.9e+08"
D35V2, continuous
D35V3, binary
                                cls
clus                              0  1
  DEL PEAK 22(17P13.1) MUTATED    9  3
  DEL PEAK 22(17P13.1) WILD-TYPE 17 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(17P13.1) MUTATED      9    3
  DEL PEAK 22(17P13.1) WILD-TYPE   17   18
        clus
vv       DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE
  FEMALE                            9                             17
  MALE                              3                             18
[1] 2 2
[1] FALSE
D35V4, binary
                                cls
clus                              0  1
  DEL PEAK 22(17P13.1) MUTATED    9  3
  DEL PEAK 22(17P13.1) WILD-TYPE 30  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(17P13.1) MUTATED      9    3
  DEL PEAK 22(17P13.1) WILD-TYPE   30    4
     clus
vv    DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE
  NO                             9                             30
  YES                            3                              4
[1] 2 2
[1] FALSE
                                vv
clus                             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK 22(17P13.1) MUTATED                                                                                   8
  DEL PEAK 22(17P13.1) WILD-TYPE                                                                                32
                                vv
clus                             PRIMARY DLBCL OF THE CNS
  DEL PEAK 22(17P13.1) MUTATED                          2
  DEL PEAK 22(17P13.1) WILD-TYPE                        1
                                vv
clus                             PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK 22(17P13.1) MUTATED                                    2
  DEL PEAK 22(17P13.1) WILD-TYPE                                  2
D35V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK 22(17P13.1) MUTATED
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                            8
  PRIMARY DLBCL OF THE CNS                                                                                     2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                           2
                                                                                   clus
vv                                                                                  DEL PEAK 22(17P13.1) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                             32
  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
  DEL PEAK 22(17P13.1) MUTATED       4                         0     8
  DEL PEAK 22(17P13.1) WILD-TYPE    14                         1    20
D35V6, multiclass
                           clus
vv                          DEL PEAK 22(17P13.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                8
                           clus
vv                          DEL PEAK 22(17P13.1) WILD-TYPE
  ASIAN                                                 14
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 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"
D35V7, binary
                                cls
clus                              0  1
  DEL PEAK 22(17P13.1) MUTATED    7  5
  DEL PEAK 22(17P13.1) WILD-TYPE  5 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(17P13.1) MUTATED      7    5
  DEL PEAK 22(17P13.1) WILD-TYPE    5   30
                        clus
vv                       DEL PEAK 22(17P13.1) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                            5
                        clus
vv                       DEL PEAK 22(17P13.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             30
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 23(17Q24.1) MUTATION ANALYSIS
D36V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 23(17Q24.1) MUTATED    5  2
  DEL PEAK 23(17Q24.1) WILD-TYPE 33  7
  DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE 
                             7                             40 
  DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE 
                             2                              7 
$`DEL PEAK 23(17Q24.1) MUTATED`
TCGA-FA-A4XK TCGA-FM-8000 TCGA-G8-6907 TCGA-GS-A9TQ TCGA-GS-A9TZ TCGA-RQ-A6JB 
       23.28        31.96        19.56        32.28        25.15         0.03 
TCGA-RQ-AAAT 
        0.56 

$`DEL PEAK 23(17Q24.1) 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-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 
       12.66        41.16        51.98        70.06       211.23       116.81 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        98.07        51.98        42.71        43.86 
TCGA-GR-A4D9 TCGA-GS-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-A9U3 TCGA-GS-A9U4 TCGA-RQ-A68N 
      109.58       111.58        12.85        25.91 

  DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE 
                          0.03                           1.91 
  DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE 
                         32.28                         211.23 
  DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE 
                        23.280                         31.415 
[1] "0.0 - 32.3 (23.3)"  "1.9 - 211.2 (31.4)"
[1] "hr=" "3.4"
D36V2, continuous
D36V3, binary
                                cls
clus                              0  1
  DEL PEAK 23(17Q24.1) MUTATED    5  2
  DEL PEAK 23(17Q24.1) WILD-TYPE 21 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(17Q24.1) MUTATED      5    2
  DEL PEAK 23(17Q24.1) WILD-TYPE   21   19
        clus
vv       DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE
  FEMALE                            5                             21
  MALE                              2                             19
[1] 2 2
[1] FALSE
D36V4, binary
                                cls
clus                              0  1
  DEL PEAK 23(17Q24.1) MUTATED    5  1
  DEL PEAK 23(17Q24.1) WILD-TYPE 34  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(17Q24.1) MUTATED      5    1
  DEL PEAK 23(17Q24.1) WILD-TYPE   34    6
     clus
vv    DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE
  NO                             5                             34
  YES                            1                              6
[1] 2 2
[1] FALSE
                                vv
clus                             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK 23(17Q24.1) MUTATED                                                                                   4
  DEL PEAK 23(17Q24.1) WILD-TYPE                                                                                36
                                vv
clus                             PRIMARY DLBCL OF THE CNS
  DEL PEAK 23(17Q24.1) MUTATED                          2
  DEL PEAK 23(17Q24.1) WILD-TYPE                        1
                                vv
clus                             PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK 23(17Q24.1) MUTATED                                    1
  DEL PEAK 23(17Q24.1) WILD-TYPE                                  3
D36V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK 23(17Q24.1) 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                                                                                  DEL PEAK 23(17Q24.1) 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                                                                             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
  DEL PEAK 23(17Q24.1) MUTATED       1                         0     6
  DEL PEAK 23(17Q24.1) WILD-TYPE    17                         1    22
D36V6, multiclass
                           clus
vv                          DEL PEAK 23(17Q24.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                6
                           clus
vv                          DEL PEAK 23(17Q24.1) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 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"
D36V7, binary
                                cls
clus                              0  1
  DEL PEAK 23(17Q24.1) MUTATED    3  4
  DEL PEAK 23(17Q24.1) WILD-TYPE  9 31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(17Q24.1) MUTATED      3    4
  DEL PEAK 23(17Q24.1) WILD-TYPE    9   31
                        clus
vv                       DEL PEAK 23(17Q24.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                            4
                        clus
vv                       DEL PEAK 23(17Q24.1) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                             31
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 24(19P13.2) MUTATION ANALYSIS
D37V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 24(19P13.2) MUTATED    4  0
  DEL PEAK 24(19P13.2) WILD-TYPE 34  9
  DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE 
                             4                             43 
  DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE 
                             0                              9 
$`DEL PEAK 24(19P13.2) MUTATED`
TCGA-FF-A7CX TCGA-GR-A4D4 TCGA-GS-A9U3 TCGA-RQ-A68N 
       12.66        51.98       111.58        25.91 

$`DEL PEAK 24(19P13.2) 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-G8-6906 
       26.01        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-A4D5 
       19.56       116.81       196.60       150.51        98.07        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV 
       43.86        57.17        32.28        38.24       128.12        24.00 
TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U4 TCGA-RQ-A6JB 
       53.16        45.14       109.58        25.15        12.85         0.03 
TCGA-RQ-AAAT 
        0.56 

  DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE 
                         12.66                           0.03 
  DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE 
                        111.58                         211.23 
  DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE 
                        38.945                         27.350 
[1] "12.7 - 111.6 (38.9)" "0.0 - 211.2 (27.4)" 
[1] "hr="     "7.7e+07"
D37V2, continuous
D37V3, binary
                                cls
clus                              0  1
  DEL PEAK 24(19P13.2) MUTATED    2  2
  DEL PEAK 24(19P13.2) WILD-TYPE 24 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(19P13.2) MUTATED      2    2
  DEL PEAK 24(19P13.2) WILD-TYPE   24   19
        clus
vv       DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE
  FEMALE                            2                             24
  MALE                              2                             19
[1] 2 2
[1] FALSE
D37V4, binary
                                cls
clus                              0  1
  DEL PEAK 24(19P13.2) MUTATED    4  0
  DEL PEAK 24(19P13.2) WILD-TYPE 35  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(19P13.2) MUTATED      4    0
  DEL PEAK 24(19P13.2) WILD-TYPE   35    7
     clus
vv    DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE
  NO                             4                             35
  YES                            0                              7
[1] 2 2
[1] FALSE
                                vv
clus                             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK 24(19P13.2) MUTATED                                                                                   3
  DEL PEAK 24(19P13.2) WILD-TYPE                                                                                37
                                vv
clus                             PRIMARY DLBCL OF THE CNS
  DEL PEAK 24(19P13.2) MUTATED                          1
  DEL PEAK 24(19P13.2) WILD-TYPE                        2
                                vv
clus                             PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK 24(19P13.2) MUTATED                                    0
  DEL PEAK 24(19P13.2) WILD-TYPE                                  4
D37V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK 24(19P13.2) 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                                                                                  DEL PEAK 24(19P13.2) 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
  DEL PEAK 24(19P13.2) MUTATED       1                         0     3
  DEL PEAK 24(19P13.2) WILD-TYPE    17                         1    25
D37V6, multiclass
                           clus
vv                          DEL PEAK 24(19P13.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                3
                           clus
vv                          DEL PEAK 24(19P13.2) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 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"
D37V7, binary
                                cls
clus                              0  1
  DEL PEAK 24(19P13.2) MUTATED    2  2
  DEL PEAK 24(19P13.2) WILD-TYPE 10 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(19P13.2) MUTATED      2    2
  DEL PEAK 24(19P13.2) WILD-TYPE   10   33
                        clus
vv                       DEL PEAK 24(19P13.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                            2
                        clus
vv                       DEL PEAK 24(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                             33
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 25(19Q13.2) MUTATION ANALYSIS
D38V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 25(19Q13.2) MUTATED    5  0
  DEL PEAK 25(19Q13.2) WILD-TYPE 33  9
  DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE 
                             5                             42 
  DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE 
                             0                              9 
$`DEL PEAK 25(19Q13.2) MUTATED`
TCGA-FF-8042 TCGA-FF-A7CX TCGA-GR-A4D9 TCGA-GS-A9TY TCGA-GS-A9U3 
       31.10        12.66        57.17       109.58       111.58 

$`DEL PEAK 25(19Q13.2) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 
        8.15        14.04        18.18        35.54        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-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-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       43.86        32.28        38.24       128.12        24.00        53.16 
TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       45.14        25.15        12.85        25.91         0.03         0.56 

  DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE 
                         12.66                           0.03 
  DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE 
                        111.58                         211.23 
  DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE 
                         57.17                          25.96 
[1] "12.7 - 111.6 (57.2)" "0.0 - 211.2 (26.0)" 
[1] "hr="     "8.2e+07"
D38V2, continuous
D38V3, binary
                                cls
clus                              0  1
  DEL PEAK 25(19Q13.2) MUTATED    4  1
  DEL PEAK 25(19Q13.2) WILD-TYPE 22 20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(19Q13.2) MUTATED      4    1
  DEL PEAK 25(19Q13.2) WILD-TYPE   22   20
        clus
vv       DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE
  FEMALE                            4                             22
  MALE                              1                             20
[1] 2 2
[1] FALSE
D38V4, binary
                                cls
clus                              0  1
  DEL PEAK 25(19Q13.2) MUTATED    5  0
  DEL PEAK 25(19Q13.2) WILD-TYPE 34  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(19Q13.2) MUTATED      5    0
  DEL PEAK 25(19Q13.2) WILD-TYPE   34    7
     clus
vv    DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE
  NO                             5                             34
  YES                            0                              7
[1] 2 2
[1] FALSE
                                vv
clus                             DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK 25(19Q13.2) MUTATED                                                                                   5
  DEL PEAK 25(19Q13.2) WILD-TYPE                                                                                35
                                vv
clus                             PRIMARY DLBCL OF THE CNS
  DEL PEAK 25(19Q13.2) MUTATED                          0
  DEL PEAK 25(19Q13.2) WILD-TYPE                        3
                                vv
clus                             PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK 25(19Q13.2) MUTATED                                    0
  DEL PEAK 25(19Q13.2) WILD-TYPE                                  4
D38V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK 25(19Q13.2) 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                                                                                  DEL PEAK 25(19Q13.2) 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
  DEL PEAK 25(19Q13.2) MUTATED       2                         0     3
  DEL PEAK 25(19Q13.2) WILD-TYPE    16                         1    25
D38V6, multiclass
                           clus
vv                          DEL PEAK 25(19Q13.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                3
                           clus
vv                          DEL PEAK 25(19Q13.2) WILD-TYPE
  ASIAN                                                 16
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 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"
D38V7, binary
                                cls
clus                              0  1
  DEL PEAK 25(19Q13.2) MUTATED    2  3
  DEL PEAK 25(19Q13.2) WILD-TYPE 10 32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(19Q13.2) MUTATED      2    3
  DEL PEAK 25(19Q13.2) WILD-TYPE   10   32
                        clus
vv                       DEL PEAK 25(19Q13.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                            3
                        clus
vv                       DEL PEAK 25(19Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                             32
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 26(22Q13.31) MUTATION ANALYSIS
D39V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 26(22Q13.31) MUTATED    6  1
  DEL PEAK 26(22Q13.31) WILD-TYPE 32  8
  DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE 
                              7                              40 
  DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE 
                              1                               8 
$`DEL PEAK 26(22Q13.31) MUTATED`
TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8043 TCGA-G8-6325 TCGA-GS-A9TQ 
       24.62         8.15        14.04        31.73        51.98        32.28 
TCGA-GS-A9TX 
       45.14 

$`DEL PEAK 26(22Q13.31) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A86F 
        4.34         4.34        23.28         1.91        23.64        18.18 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.10        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66        31.96        41.16 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       70.06       211.23        19.56       116.81       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-GS-A9TT 
       98.07        51.98        42.71        43.86        57.17        38.24 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TY TCGA-GS-A9TZ TCGA-GS-A9U3 
      128.12        24.00        53.16       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 

  DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE 
                           8.15                            0.03 
  DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE 
                          51.98                          211.23 
  DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE 
                          31.73                           26.68 
[1] "8.2 - 52.0 (31.7)"  "0.0 - 211.2 (26.7)"
[1] "hr=" "1.1"
D39V2, continuous
D39V3, binary
                                 cls
clus                               0  1
  DEL PEAK 26(22Q13.31) MUTATED    5  2
  DEL PEAK 26(22Q13.31) WILD-TYPE 21 19
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(22Q13.31) MUTATED      5    2
  DEL PEAK 26(22Q13.31) WILD-TYPE   21   19
        clus
vv       DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE
  FEMALE                             5                              21
  MALE                               2                              19
[1] 2 2
[1] FALSE
D39V4, binary
                                 cls
clus                               0  1
  DEL PEAK 26(22Q13.31) MUTATED    6  1
  DEL PEAK 26(22Q13.31) WILD-TYPE 33  6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(22Q13.31) MUTATED      6    1
  DEL PEAK 26(22Q13.31) WILD-TYPE   33    6
     clus
vv    DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE
  NO                              6                              33
  YES                             1                               6
[1] 2 2
[1] FALSE
                                 vv
clus                              DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK 26(22Q13.31) MUTATED                                                                                   7
  DEL PEAK 26(22Q13.31) WILD-TYPE                                                                                33
                                 vv
clus                              PRIMARY DLBCL OF THE CNS
  DEL PEAK 26(22Q13.31) MUTATED                          0
  DEL PEAK 26(22Q13.31) WILD-TYPE                        3
                                 vv
clus                              PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK 26(22Q13.31) MUTATED                                    0
  DEL PEAK 26(22Q13.31) WILD-TYPE                                  4
D39V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK 26(22Q13.31) 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                                                                                  DEL PEAK 26(22Q13.31) WILD-TYPE
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)                              33
  PRIMARY DLBCL OF THE CNS                                                                                        3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(22Q13.31) MUTATED       4                         0     3
  DEL PEAK 26(22Q13.31) WILD-TYPE    14                         1    25
D39V6, multiclass
                           clus
vv                          DEL PEAK 26(22Q13.31) MUTATED
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                 3
                           clus
vv                          DEL PEAK 26(22Q13.31) WILD-TYPE
  ASIAN                                                  14
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  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"
D39V7, binary
                                 cls
clus                               0  1
  DEL PEAK 26(22Q13.31) MUTATED    2  5
  DEL PEAK 26(22Q13.31) WILD-TYPE 10 30
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(22Q13.31) MUTATED      2    5
  DEL PEAK 26(22Q13.31) WILD-TYPE   10   30
                        clus
vv                       DEL PEAK 26(22Q13.31) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                             5
                        clus
vv                       DEL PEAK 26(22Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                  10
  NOT HISPANIC OR LATINO                              30
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 27(XQ28) MUTATION ANALYSIS
D40V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 27(XQ28) MUTATED    2  1
  DEL PEAK 27(XQ28) WILD-TYPE 36  8
  DEL PEAK 27(XQ28) MUTATED DEL PEAK 27(XQ28) WILD-TYPE 
                          3                          44 
  DEL PEAK 27(XQ28) MUTATED DEL PEAK 27(XQ28) WILD-TYPE 
                          1                           8 
$`DEL PEAK 27(XQ28) MUTATED`
TCGA-FA-A7Q1 TCGA-FF-8047 TCGA-GS-A9TY 
        8.15         4.14       109.58 

$`DEL PEAK 27(XQ28) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        23.28         1.91        24.62        23.64 
TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       14.04        18.18        35.54        31.10        31.73        24.69 
TCGA-FF-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-A68N 
       53.16        45.14        25.15       111.58        12.85        25.91 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

  DEL PEAK 27(XQ28) MUTATED DEL PEAK 27(XQ28) WILD-TYPE 
                       4.14                        0.03 
  DEL PEAK 27(XQ28) MUTATED DEL PEAK 27(XQ28) WILD-TYPE 
                     109.58                      211.23 
  DEL PEAK 27(XQ28) MUTATED DEL PEAK 27(XQ28) WILD-TYPE 
                      8.150                      29.225 
[1] "4.1 - 109.6 (8.2)"  "0.0 - 211.2 (29.2)"
[1] "hr=" "4"  
D40V2, continuous
D40V3, binary
                             cls
clus                           0  1
  DEL PEAK 27(XQ28) MUTATED    3  0
  DEL PEAK 27(XQ28) WILD-TYPE 23 21
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 27(XQ28) MUTATED      3    0
  DEL PEAK 27(XQ28) WILD-TYPE   23   21
        clus
vv       DEL PEAK 27(XQ28) MUTATED DEL PEAK 27(XQ28) WILD-TYPE
  FEMALE                         3                          23
  MALE                           0                          21
[1] 2 2
[1] FALSE
D40V4, binary
                             cls
clus                           0  1
  DEL PEAK 27(XQ28) MUTATED    3  0
  DEL PEAK 27(XQ28) WILD-TYPE 36  7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 27(XQ28) MUTATED      3    0
  DEL PEAK 27(XQ28) WILD-TYPE   36    7
     clus
vv    DEL PEAK 27(XQ28) MUTATED DEL PEAK 27(XQ28) WILD-TYPE
  NO                          3                          36
  YES                         0                           7
[1] 2 2
[1] FALSE
                             vv
clus                          DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  DEL PEAK 27(XQ28) MUTATED                                                                                   3
  DEL PEAK 27(XQ28) WILD-TYPE                                                                                37
                             vv
clus                          PRIMARY DLBCL OF THE CNS
  DEL PEAK 27(XQ28) MUTATED                          0
  DEL PEAK 27(XQ28) WILD-TYPE                        3
                             vv
clus                          PRIMARY MEDIASTINAL (THYMIC) DLBCL
  DEL PEAK 27(XQ28) MUTATED                                    0
  DEL PEAK 27(XQ28) WILD-TYPE                                  4
D40V5, multiclass
                                                                                   clus
vv                                                                                  DEL PEAK 27(XQ28) 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                                                                                  DEL PEAK 27(XQ28) 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
  DEL PEAK 27(XQ28) MUTATED       2                         0     1
  DEL PEAK 27(XQ28) WILD-TYPE    16                         1    27
D40V6, multiclass
                           clus
vv                          DEL PEAK 27(XQ28) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                             1
                           clus
vv                          DEL PEAK 27(XQ28) WILD-TYPE
  ASIAN                                              16
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              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"
D40V7, binary
                             cls
clus                           0  1
  DEL PEAK 27(XQ28) MUTATED    1  2
  DEL PEAK 27(XQ28) WILD-TYPE 11 33
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 27(XQ28) MUTATED      1    2
  DEL PEAK 27(XQ28) WILD-TYPE   11   33
                        clus
vv                       DEL PEAK 27(XQ28) MUTATED DEL PEAK 27(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             1                          11
  NOT HISPANIC OR LATINO                         2                          33
[1] 2 2
[1] FALSE
