[1] "ofn"        "-oTTHYM-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/THYM-TP/22507339/THYM-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THYM-TP/22516313/transformed.cor.cli.txt"

nPatients in clinical file=124, in cluster file=123, common to both=123
[1]  18 123
[1] "AMP PEAK 1(1Q41) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(1Q41) MUTATED AMP PEAK 1(1Q41) WILD-TYPE 
                        28                         95 
  AMP PEAK 1(1Q41) MUTATED AMP PEAK 1(1Q41) WILD-TYPE 
                        28                         95 
[1] "AMP PEAK 2(10Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(10Q11.21) MUTATED AMP PEAK 2(10Q11.21) WILD-TYPE 
                             3                            120 
  AMP PEAK 2(10Q11.21) MUTATED AMP PEAK 2(10Q11.21) WILD-TYPE 
                             3                            120 
[1] "AMP PEAK 3(12P12.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 3(12P12.3) MUTATED AMP PEAK 3(12P12.3) WILD-TYPE 
                            6                           117 
  AMP PEAK 3(12P12.3) MUTATED AMP PEAK 3(12P12.3) WILD-TYPE 
                            6                           117 
[1] "AMP PEAK 4(17Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 4(17Q11.2) MUTATED AMP PEAK 4(17Q11.2) WILD-TYPE 
                           10                           113 
  AMP PEAK 4(17Q11.2) MUTATED AMP PEAK 4(17Q11.2) WILD-TYPE 
                           10                           113 
[1] "AMP PEAK 5(21Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 5(21Q22.2) MUTATED AMP PEAK 5(21Q22.2) WILD-TYPE 
                            3                           120 
  AMP PEAK 5(21Q22.2) MUTATED AMP PEAK 5(21Q22.2) WILD-TYPE 
                            3                           120 
[1] "AMP PEAK 6(XP11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 6(XP11.22) MUTATED AMP PEAK 6(XP11.22) WILD-TYPE 
                            3                           120 
  AMP PEAK 6(XP11.22) MUTATED AMP PEAK 6(XP11.22) WILD-TYPE 
                            3                           120 
[1] "AMP PEAK 7(XQ23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 7(XQ23) MUTATED AMP PEAK 7(XQ23) WILD-TYPE 
                         7                        116 
  AMP PEAK 7(XQ23) MUTATED AMP PEAK 7(XQ23) WILD-TYPE 
                         7                        116 
[1] "DEL PEAK  1(2Q37.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE 
                            5                           118 
  DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE 
                            5                           118 
[1] "DEL PEAK  2(3P22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE 
                           14                           109 
  DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE 
                           14                           109 
[1] "DEL PEAK  3(6P25.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE 
                           26                            97 
  DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE 
                           26                            97 
[1] "DEL PEAK  4(6Q21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE 
                         20                         103 
  DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE 
                         20                         103 
[1] "DEL PEAK  5(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE 
                            3                           120 
  DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE 
                            3                           120 
[1] "DEL PEAK  6(9P22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(9P22.1) MUTATED DEL PEAK  6(9P22.1) WILD-TYPE 
                            6                           117 
  DEL PEAK  6(9P22.1) MUTATED DEL PEAK  6(9P22.1) WILD-TYPE 
                            6                           117 
[1] "DEL PEAK  7(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE 
                           11                           112 
  DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE 
                           11                           112 
[1] "DEL PEAK  8(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE 
                             6                            117 
  DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE 
                             6                            117 
[1] "DEL PEAK  9(19P13.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(19P13.11) MUTATED DEL PEAK  9(19P13.11) WILD-TYPE 
                              5                             118 
  DEL PEAK  9(19P13.11) MUTATED DEL PEAK  9(19P13.11) WILD-TYPE 
                              5                             118 
[1] "DEL PEAK 10(22Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(22Q12.1) MUTATED DEL PEAK 10(22Q12.1) WILD-TYPE 
                            19                            104 
  DEL PEAK 10(22Q12.1) MUTATED DEL PEAK 10(22Q12.1) WILD-TYPE 
                            19                            104 
[1] "DEL PEAK 11(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(22Q13.32) MUTATED DEL PEAK 11(22Q13.32) WILD-TYPE 
                             15                             108 
  DEL PEAK 11(22Q13.32) MUTATED DEL PEAK 11(22Q13.32) WILD-TYPE 
                             15                             108 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RACE"                                
[15] "ETHNICITY"                           

Input Data has 15 rows and 123 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=49,	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=110,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'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 123 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"    "TUMOR_TISSUE_SITE" "GENDER"           
[4] "RADIATION_THERAPY" "HISTOLOGICAL_TYPE" "RACE"             
[7] "ETHNICITY"        
YEARS_TO_BIRTH, nv=49, binary=FALSE, numeric=TRUE
TUMOR_TISSUE_SITE, nv=2, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=6, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK 1(1Q41) MUTATION ANALYSIS
D1V1, survival
                            sevent
clus2                         0  1
  AMP PEAK 1(1Q41) MUTATED   22  6
  AMP PEAK 1(1Q41) WILD-TYPE 91  3
  AMP PEAK 1(1Q41) MUTATED AMP PEAK 1(1Q41) WILD-TYPE 
                        28                         94 
  AMP PEAK 1(1Q41) MUTATED AMP PEAK 1(1Q41) WILD-TYPE 
                         6                          3 
$`AMP PEAK 1(1Q41) MUTATED`
TCGA-XM-A8RD TCGA-XM-AAZ1 TCGA-3G-AB0T TCGA-3S-A8YW TCGA-4V-A9QN TCGA-4V-A9QR 
       50.83        13.05        81.80        21.14        31.89        25.64 
TCGA-4V-A9QS TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-X7-A8D7 TCGA-X7-A8M3 
       25.45        49.41        27.45        23.47        10.68         1.64 
TCGA-XU-A92Y TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-A936 
      114.67        82.65        52.90        70.65        58.82        21.14 
TCGA-XU-AAXW TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-YT-A95G TCGA-ZB-A961 TCGA-ZB-A966 
      123.68        62.17        50.53        49.78         5.92        12.46 
TCGA-ZB-A96F TCGA-ZB-A96I TCGA-ZB-A96V TCGA-ZC-AAA7 
       57.90        54.35        30.64        28.04 

$`AMP PEAK 1(1Q41) WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RG TCGA-XU-A92Q TCGA-YT-A95F 
       95.67        23.57        15.09        12.69        35.90        25.48 
TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB14 
       26.83        71.11        45.63        68.58        59.15        25.48 
TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       15.35        18.77        34.52        96.53        93.67        62.73 
TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       41.19        51.68        26.73        20.61        20.71        14.27 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-5K-AAAP TCGA-5U-AB0E TCGA-5V-A9RR 
       21.99        12.89        68.12        34.65        22.59        27.19 
TCGA-X7-A8D6 TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE 
      138.90         1.91        65.49        59.11        36.62        32.25 
TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 
       29.62        22.85        23.18         9.50        14.50        42.15 
TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 
      125.19        54.08       150.41        64.83        83.28        40.11 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF 
       52.54        48.92        37.61        97.41        13.87        26.20 
TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O 
       11.93        12.72        84.23        32.25        37.81       112.11 
TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X 
       90.05        45.24       149.98         4.08       107.80        77.03 
TCGA-XU-A92Z TCGA-XU-AAXX TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E 
      120.43        89.46        49.38       107.44        24.66        35.18 
TCGA-YT-A95H TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A969 TCGA-ZB-A96A 
       23.38        54.15        48.72        42.31        34.39        77.39 
TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96L 
       72.69        64.44        59.80        52.80        49.45        50.27 
TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZC-AAAA 
        0.46        34.52        24.76        22.19        59.31        26.93 
TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       38.30        16.34        68.91        45.96 

  AMP PEAK 1(1Q41) MUTATED AMP PEAK 1(1Q41) WILD-TYPE 
                      1.64                       0.46 
  AMP PEAK 1(1Q41) MUTATED AMP PEAK 1(1Q41) WILD-TYPE 
                    123.68                     150.41 
  AMP PEAK 1(1Q41) MUTATED AMP PEAK 1(1Q41) WILD-TYPE 
                     40.65                      40.65 
[1] "1.6 - 123.7 (40.6)" "0.5 - 150.4 (40.6)"
[1] "hr=" "7.2"
D1V2, continuous
D1V3, binary
                            cls
clus                          0  1
  AMP PEAK 1(1Q41) MUTATED    6 22
  AMP PEAK 1(1Q41) WILD-TYPE 21 74
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 1(1Q41) MUTATED      6   22
  AMP PEAK 1(1Q41) WILD-TYPE   21   74
                      clus
vv                     AMP PEAK 1(1Q41) MUTATED AMP PEAK 1(1Q41) WILD-TYPE
  ANTERIOR MEDIASTINUM                        6                         21
  THYMUS                                     22                         74
[1] 2 2
[1] FALSE
D1V4, binary
                            cls
clus                          0  1
  AMP PEAK 1(1Q41) MUTATED   17 11
  AMP PEAK 1(1Q41) WILD-TYPE 42 53
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 1(1Q41) MUTATED     17   11
  AMP PEAK 1(1Q41) WILD-TYPE   42   53
        clus
vv       AMP PEAK 1(1Q41) MUTATED AMP PEAK 1(1Q41) WILD-TYPE
  FEMALE                       17                         42
  MALE                         11                         53
[1] 2 2
[1] FALSE
D1V5, binary
                            cls
clus                          0  1
  AMP PEAK 1(1Q41) MUTATED   10 18
  AMP PEAK 1(1Q41) WILD-TYPE 71 24
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 1(1Q41) MUTATED     10   18
  AMP PEAK 1(1Q41) WILD-TYPE   71   24
     clus
vv    AMP PEAK 1(1Q41) MUTATED AMP PEAK 1(1Q41) WILD-TYPE
  NO                        10                         71
  YES                       18                         24
[1] 2 2
[1] FALSE
                            vv
clus                         THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  AMP PEAK 1(1Q41) MUTATED                 1                2                2
  AMP PEAK 1(1Q41) WILD-TYPE              16               36               13
                            vv
clus                         THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  AMP PEAK 1(1Q41) MUTATED                  8                7               8
  AMP PEAK 1(1Q41) WILD-TYPE               22                5               3
D1V6, multiclass
                  clus
vv                 AMP PEAK 1(1Q41) MUTATED AMP PEAK 1(1Q41) WILD-TYPE
  THYMOMA; TYPE A                         1                         16
  THYMOMA; TYPE AB                        2                         36
  THYMOMA; TYPE B1                        2                         13
  THYMOMA; TYPE B2                        8                         22
  THYMOMA; TYPE B3                        7                          5
  THYMOMA; TYPE C                         8                          3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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(1Q41) MUTATED       3                         1    24
  AMP PEAK 1(1Q41) WILD-TYPE    10                         5    78
D1V7, multiclass
                           clus
vv                          AMP PEAK 1(1Q41) MUTATED AMP PEAK 1(1Q41) WILD-TYPE
  ASIAN                                            3                         10
  BLACK OR AFRICAN AMERICAN                        1                          5
  WHITE                                           24                         78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
                            cls
clus                          0  1
  AMP PEAK 1(1Q41) MUTATED    3 23
  AMP PEAK 1(1Q41) WILD-TYPE  6 77
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 1(1Q41) MUTATED      3   23
  AMP PEAK 1(1Q41) WILD-TYPE    6   77
                        clus
vv                       AMP PEAK 1(1Q41) MUTATED AMP PEAK 1(1Q41) WILD-TYPE
  HISPANIC OR LATINO                            3                          6
  NOT HISPANIC OR LATINO                       23                         77
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK 2(10Q11.21) MUTATION ANALYSIS
D2V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 2(10Q11.21) MUTATED     3   0
  AMP PEAK 2(10Q11.21) WILD-TYPE 110   9
  AMP PEAK 2(10Q11.21) MUTATED AMP PEAK 2(10Q11.21) WILD-TYPE 
                             3                            119 
  AMP PEAK 2(10Q11.21) MUTATED AMP PEAK 2(10Q11.21) WILD-TYPE 
                             0                              9 
$`AMP PEAK 2(10Q11.21) MUTATED`
TCGA-4V-A9QR TCGA-X7-A8M0 TCGA-XU-A933 
       25.64        14.50        58.82 

$`AMP PEAK 2(10Q11.21) WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XM-AAZ1 
       95.67        23.57        15.09        50.83        12.69        13.05 
TCGA-XU-A92Q TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O 
       35.90        25.48        26.83        71.11        45.63        68.58 
TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-3S-AAYX 
       59.15        81.80        25.48        15.35        21.14        18.77 
TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN 
       34.52        96.53        93.67        62.73        41.19        31.89 
TCGA-4V-A9QQ TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       51.68        25.45        26.73        20.61        20.71        14.27 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP 
       21.99        12.89        68.12        49.41        27.45        34.65 
TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 
       23.47        22.59        27.19       138.90        10.68         1.91 
TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG 
       65.49        59.11        36.62        32.25        29.62        22.85 
TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 
       23.18         9.50        42.15         1.64       125.19        54.08 
TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
      150.41        64.83        83.28        40.11        52.54        48.92 
TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI 
       37.61        97.41        13.87        26.20        11.93        12.72 
TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T 
       84.23        32.25        37.81       112.11        90.05        45.24 
TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A92Z 
      149.98         4.08       107.80        77.03       114.67       120.43 
TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A936 TCGA-XU-AAXW TCGA-XU-AAXX 
       82.65        52.90        70.65        21.14       123.68        89.46 
TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E 
       62.17        50.53        49.38       107.44        24.66        35.18 
TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 
       49.78        23.38         5.92        54.15        48.72        42.31 
TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       12.46        34.39        77.39        72.69        64.44        59.80 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M 
       57.90        52.80        49.45        54.35        50.27         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 
       34.52        24.76        22.19        59.31        30.64        28.04 
TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       26.93        38.30        16.34        68.91        45.96 

  AMP PEAK 2(10Q11.21) MUTATED AMP PEAK 2(10Q11.21) WILD-TYPE 
                         14.50                           0.46 
  AMP PEAK 2(10Q11.21) MUTATED AMP PEAK 2(10Q11.21) WILD-TYPE 
                         58.82                         150.41 
  AMP PEAK 2(10Q11.21) MUTATED AMP PEAK 2(10Q11.21) WILD-TYPE 
                         25.64                          41.19 
[1] "14.5 - 58.8 (25.6)" "0.5 - 150.4 (41.2)"
[1] "hr="     "9200000"
D2V2, continuous
D2V3, binary
                                cls
clus                              0  1
  AMP PEAK 2(10Q11.21) MUTATED    0  3
  AMP PEAK 2(10Q11.21) WILD-TYPE 27 93
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 2(10Q11.21) MUTATED      0    3
  AMP PEAK 2(10Q11.21) WILD-TYPE   27   93
                      clus
vv                     AMP PEAK 2(10Q11.21) MUTATED
  ANTERIOR MEDIASTINUM                            0
  THYMUS                                          3
                      clus
vv                     AMP PEAK 2(10Q11.21) WILD-TYPE
  ANTERIOR MEDIASTINUM                             27
  THYMUS                                           93
[1] 2 2
[1] FALSE
D2V4, binary
                                cls
clus                              0  1
  AMP PEAK 2(10Q11.21) MUTATED    3  0
  AMP PEAK 2(10Q11.21) WILD-TYPE 56 64
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 2(10Q11.21) MUTATED      3    0
  AMP PEAK 2(10Q11.21) WILD-TYPE   56   64
        clus
vv       AMP PEAK 2(10Q11.21) MUTATED AMP PEAK 2(10Q11.21) WILD-TYPE
  FEMALE                            3                             56
  MALE                              0                             64
[1] 2 2
[1] FALSE
D2V5, binary
                                cls
clus                              0  1
  AMP PEAK 2(10Q11.21) MUTATED    1  2
  AMP PEAK 2(10Q11.21) WILD-TYPE 80 40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 2(10Q11.21) MUTATED      1    2
  AMP PEAK 2(10Q11.21) WILD-TYPE   80   40
     clus
vv    AMP PEAK 2(10Q11.21) MUTATED AMP PEAK 2(10Q11.21) WILD-TYPE
  NO                             1                             80
  YES                            2                             40
[1] 2 2
[1] FALSE
                                vv
clus                             THYMOMA; TYPE A THYMOMA; TYPE AB
  AMP PEAK 2(10Q11.21) MUTATED                 0                0
  AMP PEAK 2(10Q11.21) WILD-TYPE              17               38
                                vv
clus                             THYMOMA; TYPE B1 THYMOMA; TYPE B2
  AMP PEAK 2(10Q11.21) MUTATED                  0                1
  AMP PEAK 2(10Q11.21) WILD-TYPE               15               29
                                vv
clus                             THYMOMA; TYPE B3 THYMOMA; TYPE C
  AMP PEAK 2(10Q11.21) MUTATED                  1               1
  AMP PEAK 2(10Q11.21) WILD-TYPE               11              10
D2V6, multiclass
                  clus
vv                 AMP PEAK 2(10Q11.21) MUTATED AMP PEAK 2(10Q11.21) WILD-TYPE
  THYMOMA; TYPE A                             0                             17
  THYMOMA; TYPE AB                            0                             38
  THYMOMA; TYPE B1                            0                             15
  THYMOMA; TYPE B2                            1                             29
  THYMOMA; TYPE B3                            1                             11
  THYMOMA; TYPE C                             1                             10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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(10Q11.21) MUTATED       1                         0     2
  AMP PEAK 2(10Q11.21) WILD-TYPE    12                         6   100
D2V7, multiclass
                           clus
vv                          AMP PEAK 2(10Q11.21) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                2
                           clus
vv                          AMP PEAK 2(10Q11.21) WILD-TYPE
  ASIAN                                                 12
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                                cls
clus                              0  1
  AMP PEAK 2(10Q11.21) MUTATED    0  3
  AMP PEAK 2(10Q11.21) WILD-TYPE  9 97
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 2(10Q11.21) MUTATED      0    3
  AMP PEAK 2(10Q11.21) WILD-TYPE    9   97
                        clus
vv                       AMP PEAK 2(10Q11.21) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            3
                        clus
vv                       AMP PEAK 2(10Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                             97
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK 3(12P12.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 3(12P12.3) MUTATED     5   1
  AMP PEAK 3(12P12.3) WILD-TYPE 108   8
  AMP PEAK 3(12P12.3) MUTATED AMP PEAK 3(12P12.3) WILD-TYPE 
                            6                           116 
  AMP PEAK 3(12P12.3) MUTATED AMP PEAK 3(12P12.3) WILD-TYPE 
                            1                             8 
$`AMP PEAK 3(12P12.3) MUTATED`
TCGA-3S-A8YW TCGA-5U-AB0D TCGA-XM-A8R9 TCGA-XM-A8RC TCGA-XU-A936 TCGA-ZC-AAA7 
       21.14        23.47        48.92        97.41        21.14        28.04 

$`AMP PEAK 3(12P12.3) WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XM-AAZ1 
       95.67        23.57        15.09        50.83        12.69        13.05 
TCGA-XU-A92Q TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O 
       35.90        25.48        26.83        71.11        45.63        68.58 
TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L 
       59.15        81.80        25.48        15.35        18.77        34.52 
TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ 
       96.53        93.67        62.73        41.19        31.89        51.68 
TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       25.64        25.45        26.73        20.61        20.71        14.27 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP 
       21.99        12.89        68.12        49.41        27.45        34.65 
TCGA-5U-AB0E TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB 
       22.59        27.19       138.90        10.68         1.91        65.49 
TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI 
       59.11        36.62        32.25        29.62        22.85        23.18 
TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 
        9.50        14.50        42.15         1.64       125.19        54.08 
TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8RB 
      150.41        64.83        83.28        40.11        52.54        37.61 
TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 
       13.87        26.20        11.93        12.72        84.23        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
       37.81       112.11        90.05        45.24       149.98         4.08 
TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 
      107.80        77.03       114.67       120.43        82.65        52.90 
TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ 
       70.65        58.82       123.68        89.46        62.17        50.53 
TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95G TCGA-YT-A95H 
       49.38       107.44        24.66        35.18        49.78        23.38 
TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A969 
        5.92        54.15        48.72        42.31        12.46        34.39 
TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G 
       77.39        72.69        64.44        59.80        57.90        52.80 
TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
       49.45        54.35        50.27         0.46        34.52        24.76 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
       22.19        59.31        30.64        26.93        38.30        16.34 
TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       68.91        45.96 

  AMP PEAK 3(12P12.3) MUTATED AMP PEAK 3(12P12.3) WILD-TYPE 
                        21.14                          0.46 
  AMP PEAK 3(12P12.3) MUTATED AMP PEAK 3(12P12.3) WILD-TYPE 
                        97.41                        150.41 
  AMP PEAK 3(12P12.3) MUTATED AMP PEAK 3(12P12.3) WILD-TYPE 
                       25.755                        41.670 
[1] "21.1 - 97.4 (25.8)" "0.5 - 150.4 (41.7)"
[1] "hr=" "2.9"
D3V2, continuous
D3V3, binary
                               cls
clus                             0  1
  AMP PEAK 3(12P12.3) MUTATED    4  2
  AMP PEAK 3(12P12.3) WILD-TYPE 23 94
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(12P12.3) MUTATED      4    2
  AMP PEAK 3(12P12.3) WILD-TYPE   23   94
                      clus
vv                     AMP PEAK 3(12P12.3) MUTATED
  ANTERIOR MEDIASTINUM                           4
  THYMUS                                         2
                      clus
vv                     AMP PEAK 3(12P12.3) WILD-TYPE
  ANTERIOR MEDIASTINUM                            23
  THYMUS                                          94
[1] 2 2
[1] FALSE
D3V4, binary
                               cls
clus                             0  1
  AMP PEAK 3(12P12.3) MUTATED    3  3
  AMP PEAK 3(12P12.3) WILD-TYPE 56 61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(12P12.3) MUTATED      3    3
  AMP PEAK 3(12P12.3) WILD-TYPE   56   61
        clus
vv       AMP PEAK 3(12P12.3) MUTATED AMP PEAK 3(12P12.3) WILD-TYPE
  FEMALE                           3                            56
  MALE                             3                            61
[1] 2 2
[1] FALSE
D3V5, binary
                               cls
clus                             0  1
  AMP PEAK 3(12P12.3) MUTATED    4  2
  AMP PEAK 3(12P12.3) WILD-TYPE 77 40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(12P12.3) MUTATED      4    2
  AMP PEAK 3(12P12.3) WILD-TYPE   77   40
     clus
vv    AMP PEAK 3(12P12.3) MUTATED AMP PEAK 3(12P12.3) WILD-TYPE
  NO                            4                            77
  YES                           2                            40
[1] 2 2
[1] FALSE
                               vv
clus                            THYMOMA; TYPE A THYMOMA; TYPE AB
  AMP PEAK 3(12P12.3) MUTATED                 1                0
  AMP PEAK 3(12P12.3) WILD-TYPE              16               38
                               vv
clus                            THYMOMA; TYPE B1 THYMOMA; TYPE B2
  AMP PEAK 3(12P12.3) MUTATED                  0                1
  AMP PEAK 3(12P12.3) WILD-TYPE               15               29
                               vv
clus                            THYMOMA; TYPE B3 THYMOMA; TYPE C
  AMP PEAK 3(12P12.3) MUTATED                  0               4
  AMP PEAK 3(12P12.3) WILD-TYPE               12               7
D3V6, multiclass
                  clus
vv                 AMP PEAK 3(12P12.3) MUTATED AMP PEAK 3(12P12.3) WILD-TYPE
  THYMOMA; TYPE A                            1                            16
  THYMOMA; TYPE AB                           0                            38
  THYMOMA; TYPE B1                           0                            15
  THYMOMA; TYPE B2                           1                            29
  THYMOMA; TYPE B3                           0                            12
  THYMOMA; TYPE C                            4                             7
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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(12P12.3) MUTATED       0                         0     6
  AMP PEAK 3(12P12.3) WILD-TYPE    13                         6    96
D3V7, multiclass
                           clus
vv                          AMP PEAK 3(12P12.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               6
                           clus
vv                          AMP PEAK 3(12P12.3) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
                               cls
clus                             0  1
  AMP PEAK 3(12P12.3) MUTATED    2  4
  AMP PEAK 3(12P12.3) WILD-TYPE  7 96
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(12P12.3) MUTATED      2    4
  AMP PEAK 3(12P12.3) WILD-TYPE    7   96
                        clus
vv                       AMP PEAK 3(12P12.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                           4
                        clus
vv                       AMP PEAK 3(12P12.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            96
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK 4(17Q11.2) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 4(17Q11.2) MUTATED    10   0
  AMP PEAK 4(17Q11.2) WILD-TYPE 103   9
  AMP PEAK 4(17Q11.2) MUTATED AMP PEAK 4(17Q11.2) WILD-TYPE 
                           10                           112 
  AMP PEAK 4(17Q11.2) MUTATED AMP PEAK 4(17Q11.2) WILD-TYPE 
                            0                             9 
$`AMP PEAK 4(17Q11.2) MUTATED`
TCGA-XM-A8RG TCGA-3S-A8YW TCGA-4V-A9QJ TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-XM-A8RC 
       12.69        21.14        93.67        27.45        23.47        97.41 
TCGA-XU-A933 TCGA-XU-A936 TCGA-ZB-A962 TCGA-ZB-A96L 
       58.82        21.14        54.15        50.27 

$`AMP PEAK 4(17Q11.2) WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-AAZ1 TCGA-XU-A92Q 
       95.67        23.57        15.09        50.83        13.05        35.90 
TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O TCGA-3G-AB0Q 
       25.48        26.83        71.11        45.63        68.58        59.15 
TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI 
       81.80        25.48        15.35        18.77        34.52        96.53 
TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS 
       62.73        41.19        31.89        51.68        25.64        25.45 
TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA 
       26.73        20.61        20.71        14.27        21.99        12.89 
TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5K-AAAP TCGA-5U-AB0E TCGA-5V-A9RR TCGA-X7-A8D6 
       68.12        49.41        34.65        22.59        27.19       138.90 
TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE 
       10.68         1.91        65.49        59.11        36.62        32.25 
TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 
       29.62        22.85        23.18         9.50        14.50        42.15 
TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 
        1.64       125.19        54.08       150.41        64.83        83.28 
TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF 
       40.11        52.54        48.92        37.61        13.87        26.20 
TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O 
       11.93        12.72        84.23        32.25        37.81       112.11 
TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X 
       90.05        45.24       149.98         4.08       107.80        77.03 
TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-AAXW 
      114.67       120.43        82.65        52.90        70.65       123.68 
TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D 
       89.46        62.17        50.53        49.38       107.44        24.66 
TCGA-YT-A95E TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A963 TCGA-ZB-A964 
       35.18        49.78        23.38         5.92        48.72        42.31 
TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       12.46        34.39        77.39        72.69        64.44        59.80 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96M TCGA-ZB-A96O 
       57.90        52.80        49.45        54.35         0.46        34.52 
TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA 
       24.76        22.19        59.31        30.64        28.04        26.93 
TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       38.30        16.34        68.91        45.96 

  AMP PEAK 4(17Q11.2) MUTATED AMP PEAK 4(17Q11.2) WILD-TYPE 
                        12.69                          0.46 
  AMP PEAK 4(17Q11.2) MUTATED AMP PEAK 4(17Q11.2) WILD-TYPE 
                        97.41                        150.41 
  AMP PEAK 4(17Q11.2) MUTATED AMP PEAK 4(17Q11.2) WILD-TYPE 
                        38.86                         40.65 
[1] "12.7 - 97.4 (38.9)" "0.5 - 150.4 (40.6)"
[1] "hr="     "7.6e+07"
D4V2, continuous
D4V3, binary
                               cls
clus                             0  1
  AMP PEAK 4(17Q11.2) MUTATED    3  7
  AMP PEAK 4(17Q11.2) WILD-TYPE 24 89
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(17Q11.2) MUTATED      3    7
  AMP PEAK 4(17Q11.2) WILD-TYPE   24   89
                      clus
vv                     AMP PEAK 4(17Q11.2) MUTATED
  ANTERIOR MEDIASTINUM                           3
  THYMUS                                         7
                      clus
vv                     AMP PEAK 4(17Q11.2) WILD-TYPE
  ANTERIOR MEDIASTINUM                            24
  THYMUS                                          89
[1] 2 2
[1] FALSE
D4V4, binary
                               cls
clus                             0  1
  AMP PEAK 4(17Q11.2) MUTATED    5  5
  AMP PEAK 4(17Q11.2) WILD-TYPE 54 59
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(17Q11.2) MUTATED      5    5
  AMP PEAK 4(17Q11.2) WILD-TYPE   54   59
        clus
vv       AMP PEAK 4(17Q11.2) MUTATED AMP PEAK 4(17Q11.2) WILD-TYPE
  FEMALE                           5                            54
  MALE                             5                            59
[1] 2 2
[1] FALSE
D4V5, binary
                               cls
clus                             0  1
  AMP PEAK 4(17Q11.2) MUTATED    5  5
  AMP PEAK 4(17Q11.2) WILD-TYPE 76 37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(17Q11.2) MUTATED      5    5
  AMP PEAK 4(17Q11.2) WILD-TYPE   76   37
     clus
vv    AMP PEAK 4(17Q11.2) MUTATED AMP PEAK 4(17Q11.2) WILD-TYPE
  NO                            5                            76
  YES                           5                            37
[1] 2 2
[1] FALSE
                               vv
clus                            THYMOMA; TYPE A THYMOMA; TYPE AB
  AMP PEAK 4(17Q11.2) MUTATED                 2                0
  AMP PEAK 4(17Q11.2) WILD-TYPE              15               38
                               vv
clus                            THYMOMA; TYPE B1 THYMOMA; TYPE B2
  AMP PEAK 4(17Q11.2) MUTATED                  0                1
  AMP PEAK 4(17Q11.2) WILD-TYPE               15               29
                               vv
clus                            THYMOMA; TYPE B3 THYMOMA; TYPE C
  AMP PEAK 4(17Q11.2) MUTATED                  2               5
  AMP PEAK 4(17Q11.2) WILD-TYPE               10               6
D4V6, multiclass
                  clus
vv                 AMP PEAK 4(17Q11.2) MUTATED AMP PEAK 4(17Q11.2) WILD-TYPE
  THYMOMA; TYPE A                            2                            15
  THYMOMA; TYPE AB                           0                            38
  THYMOMA; TYPE B1                           0                            15
  THYMOMA; TYPE B2                           1                            29
  THYMOMA; TYPE B3                           2                            10
  THYMOMA; TYPE C                            5                             6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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(17Q11.2) MUTATED       1                         0     9
  AMP PEAK 4(17Q11.2) WILD-TYPE    12                         6    93
D4V7, multiclass
                           clus
vv                          AMP PEAK 4(17Q11.2) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               9
                           clus
vv                          AMP PEAK 4(17Q11.2) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
                               cls
clus                             0  1
  AMP PEAK 4(17Q11.2) MUTATED    2  8
  AMP PEAK 4(17Q11.2) WILD-TYPE  7 92
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(17Q11.2) MUTATED      2    8
  AMP PEAK 4(17Q11.2) WILD-TYPE    7   92
                        clus
vv                       AMP PEAK 4(17Q11.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                           8
                        clus
vv                       AMP PEAK 4(17Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            92
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK 5(21Q22.2) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 5(21Q22.2) MUTATED     3   0
  AMP PEAK 5(21Q22.2) WILD-TYPE 110   9
  AMP PEAK 5(21Q22.2) MUTATED AMP PEAK 5(21Q22.2) WILD-TYPE 
                            3                           119 
  AMP PEAK 5(21Q22.2) MUTATED AMP PEAK 5(21Q22.2) WILD-TYPE 
                            0                             9 
$`AMP PEAK 5(21Q22.2) MUTATED`
TCGA-X7-A8M3 TCGA-XU-A936 TCGA-ZB-A969 
        1.64        21.14        34.39 

$`AMP PEAK 5(21Q22.2) WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XM-AAZ1 
       95.67        23.57        15.09        50.83        12.69        13.05 
TCGA-XU-A92Q TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O 
       35.90        25.48        26.83        71.11        45.63        68.58 
TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-3S-AAYX 
       59.15        81.80        25.48        15.35        21.14        18.77 
TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN 
       34.52        96.53        93.67        62.73        41.19        31.89 
TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW 
       51.68        25.64        25.45        26.73        20.61        20.71 
TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ 
       14.27        21.99        12.89        68.12        49.41        27.45 
TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 
       34.65        23.47        22.59        27.19       138.90        10.68 
TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF 
        1.91        65.49        59.11        36.62        32.25        29.62 
TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M4 
       22.85        23.18         9.50        14.50        42.15       125.19 
TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
       54.08       150.41        64.83        83.28        40.11        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH 
       48.92        37.61        97.41        13.87        26.20        11.93 
TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R 
       12.72        84.23        32.25        37.81       112.11        90.05 
TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y 
       45.24       149.98         4.08       107.80        77.03       114.67 
TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-AAXW 
      120.43        82.65        52.90        70.65        58.82       123.68 
TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D 
       89.46        62.17        50.53        49.38       107.44        24.66 
TCGA-YT-A95E TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 
       35.18        49.78        23.38         5.92        54.15        48.72 
TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       42.31        12.46        77.39        72.69        64.44        59.80 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M 
       57.90        52.80        49.45        54.35        50.27         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 
       34.52        24.76        22.19        59.31        30.64        28.04 
TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       26.93        38.30        16.34        68.91        45.96 

  AMP PEAK 5(21Q22.2) MUTATED AMP PEAK 5(21Q22.2) WILD-TYPE 
                         1.64                          0.46 
  AMP PEAK 5(21Q22.2) MUTATED AMP PEAK 5(21Q22.2) WILD-TYPE 
                        34.39                        150.41 
  AMP PEAK 5(21Q22.2) MUTATED AMP PEAK 5(21Q22.2) WILD-TYPE 
                        21.14                         42.15 
[1] "1.6 - 34.4 (21.1)"  "0.5 - 150.4 (42.1)"
[1] "hr="     "9100000"
D5V2, continuous
D5V3, binary
                               cls
clus                             0  1
  AMP PEAK 5(21Q22.2) MUTATED    2  1
  AMP PEAK 5(21Q22.2) WILD-TYPE 25 95
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 5(21Q22.2) MUTATED      2    1
  AMP PEAK 5(21Q22.2) WILD-TYPE   25   95
                      clus
vv                     AMP PEAK 5(21Q22.2) MUTATED
  ANTERIOR MEDIASTINUM                           2
  THYMUS                                         1
                      clus
vv                     AMP PEAK 5(21Q22.2) WILD-TYPE
  ANTERIOR MEDIASTINUM                            25
  THYMUS                                          95
[1] 2 2
[1] FALSE
D5V4, binary
                               cls
clus                             0  1
  AMP PEAK 5(21Q22.2) MUTATED    3  0
  AMP PEAK 5(21Q22.2) WILD-TYPE 56 64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 5(21Q22.2) MUTATED      3    0
  AMP PEAK 5(21Q22.2) WILD-TYPE   56   64
        clus
vv       AMP PEAK 5(21Q22.2) MUTATED AMP PEAK 5(21Q22.2) WILD-TYPE
  FEMALE                           3                            56
  MALE                             0                            64
[1] 2 2
[1] FALSE
D5V5, binary
                               cls
clus                             0  1
  AMP PEAK 5(21Q22.2) MUTATED    2  1
  AMP PEAK 5(21Q22.2) WILD-TYPE 79 41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 5(21Q22.2) MUTATED      2    1
  AMP PEAK 5(21Q22.2) WILD-TYPE   79   41
     clus
vv    AMP PEAK 5(21Q22.2) MUTATED AMP PEAK 5(21Q22.2) WILD-TYPE
  NO                            2                            79
  YES                           1                            41
[1] 2 2
[1] FALSE
                               vv
clus                            THYMOMA; TYPE A THYMOMA; TYPE AB
  AMP PEAK 5(21Q22.2) MUTATED                 0                0
  AMP PEAK 5(21Q22.2) WILD-TYPE              17               38
                               vv
clus                            THYMOMA; TYPE B1 THYMOMA; TYPE B2
  AMP PEAK 5(21Q22.2) MUTATED                  0                0
  AMP PEAK 5(21Q22.2) WILD-TYPE               15               30
                               vv
clus                            THYMOMA; TYPE B3 THYMOMA; TYPE C
  AMP PEAK 5(21Q22.2) MUTATED                  1               2
  AMP PEAK 5(21Q22.2) WILD-TYPE               11               9
D5V6, multiclass
                  clus
vv                 AMP PEAK 5(21Q22.2) MUTATED AMP PEAK 5(21Q22.2) WILD-TYPE
  THYMOMA; TYPE A                            0                            17
  THYMOMA; TYPE AB                           0                            38
  THYMOMA; TYPE B1                           0                            15
  THYMOMA; TYPE B2                           0                            30
  THYMOMA; TYPE B3                           1                            11
  THYMOMA; TYPE C                            2                             9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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(21Q22.2) MUTATED       0                         0     3
  AMP PEAK 5(21Q22.2) WILD-TYPE    13                         6    99
D5V7, multiclass
                           clus
vv                          AMP PEAK 5(21Q22.2) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               3
                           clus
vv                          AMP PEAK 5(21Q22.2) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                               cls
clus                             0  1
  AMP PEAK 5(21Q22.2) MUTATED    0  3
  AMP PEAK 5(21Q22.2) WILD-TYPE  9 97
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 5(21Q22.2) MUTATED      0    3
  AMP PEAK 5(21Q22.2) WILD-TYPE    9   97
                        clus
vv                       AMP PEAK 5(21Q22.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       AMP PEAK 5(21Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                            97
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK 6(XP11.22) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 6(XP11.22) MUTATED     3   0
  AMP PEAK 6(XP11.22) WILD-TYPE 110   9
  AMP PEAK 6(XP11.22) MUTATED AMP PEAK 6(XP11.22) WILD-TYPE 
                            3                           119 
  AMP PEAK 6(XP11.22) MUTATED AMP PEAK 6(XP11.22) WILD-TYPE 
                            0                             9 
$`AMP PEAK 6(XP11.22) MUTATED`
TCGA-4V-A9QI TCGA-4V-A9QR TCGA-X7-A8M3 
       96.53        25.64         1.64 

$`AMP PEAK 6(XP11.22) WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XM-AAZ1 
       95.67        23.57        15.09        50.83        12.69        13.05 
TCGA-XU-A92Q TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O 
       35.90        25.48        26.83        71.11        45.63        68.58 
TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-3S-AAYX 
       59.15        81.80        25.48        15.35        21.14        18.77 
TCGA-3T-AA9L TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ 
       34.52        93.67        62.73        41.19        31.89        51.68 
TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 
       25.45        26.73        20.61        20.71        14.27        21.99 
TCGA-4X-A9FA TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D 
       12.89        68.12        49.41        27.45        34.65        23.47 
TCGA-5U-AB0E TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB 
       22.59        27.19       138.90        10.68         1.91        65.49 
TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI 
       59.11        36.62        32.25        29.62        22.85        23.18 
TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 
        9.50        14.50        42.15       125.19        54.08       150.41 
TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       64.83        83.28        40.11        52.54        48.92        37.61 
TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL 
       97.41        13.87        26.20        11.93        12.72        84.23 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U 
       32.25        37.81       112.11        90.05        45.24       149.98 
TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A930 
        4.08       107.80        77.03       114.67       120.43        82.65 
TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXW TCGA-XU-AAXX 
       52.90        70.65        58.82        21.14       123.68        89.46 
TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E 
       62.17        50.53        49.38       107.44        24.66        35.18 
TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 
       49.78        23.38         5.92        54.15        48.72        42.31 
TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       12.46        34.39        77.39        72.69        64.44        59.80 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M 
       57.90        52.80        49.45        54.35        50.27         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 
       34.52        24.76        22.19        59.31        30.64        28.04 
TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       26.93        38.30        16.34        68.91        45.96 

  AMP PEAK 6(XP11.22) MUTATED AMP PEAK 6(XP11.22) WILD-TYPE 
                         1.64                          0.46 
  AMP PEAK 6(XP11.22) MUTATED AMP PEAK 6(XP11.22) WILD-TYPE 
                        96.53                        150.41 
  AMP PEAK 6(XP11.22) MUTATED AMP PEAK 6(XP11.22) WILD-TYPE 
                        25.64                         41.19 
[1] "1.6 - 96.5 (25.6)"  "0.5 - 150.4 (41.2)"
[1] "hr="     "2.6e+07"
D6V2, continuous
D6V3, binary
                               cls
clus                             0  1
  AMP PEAK 6(XP11.22) MUTATED    0  3
  AMP PEAK 6(XP11.22) WILD-TYPE 27 93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(XP11.22) MUTATED      0    3
  AMP PEAK 6(XP11.22) WILD-TYPE   27   93
                      clus
vv                     AMP PEAK 6(XP11.22) MUTATED
  ANTERIOR MEDIASTINUM                           0
  THYMUS                                         3
                      clus
vv                     AMP PEAK 6(XP11.22) WILD-TYPE
  ANTERIOR MEDIASTINUM                            27
  THYMUS                                          93
[1] 2 2
[1] FALSE
D6V4, binary
                               cls
clus                             0  1
  AMP PEAK 6(XP11.22) MUTATED    2  1
  AMP PEAK 6(XP11.22) WILD-TYPE 57 63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(XP11.22) MUTATED      2    1
  AMP PEAK 6(XP11.22) WILD-TYPE   57   63
        clus
vv       AMP PEAK 6(XP11.22) MUTATED AMP PEAK 6(XP11.22) WILD-TYPE
  FEMALE                           2                            57
  MALE                             1                            63
[1] 2 2
[1] FALSE
D6V5, binary
                               cls
clus                             0  1
  AMP PEAK 6(XP11.22) MUTATED    1  2
  AMP PEAK 6(XP11.22) WILD-TYPE 80 40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(XP11.22) MUTATED      1    2
  AMP PEAK 6(XP11.22) WILD-TYPE   80   40
     clus
vv    AMP PEAK 6(XP11.22) MUTATED AMP PEAK 6(XP11.22) WILD-TYPE
  NO                            1                            80
  YES                           2                            40
[1] 2 2
[1] FALSE
                               vv
clus                            THYMOMA; TYPE A THYMOMA; TYPE AB
  AMP PEAK 6(XP11.22) MUTATED                 0                0
  AMP PEAK 6(XP11.22) WILD-TYPE              17               38
                               vv
clus                            THYMOMA; TYPE B1 THYMOMA; TYPE B2
  AMP PEAK 6(XP11.22) MUTATED                  0                1
  AMP PEAK 6(XP11.22) WILD-TYPE               15               29
                               vv
clus                            THYMOMA; TYPE B3 THYMOMA; TYPE C
  AMP PEAK 6(XP11.22) MUTATED                  2               0
  AMP PEAK 6(XP11.22) WILD-TYPE               10              11
D6V6, multiclass
                  clus
vv                 AMP PEAK 6(XP11.22) MUTATED AMP PEAK 6(XP11.22) WILD-TYPE
  THYMOMA; TYPE A                            0                            17
  THYMOMA; TYPE AB                           0                            38
  THYMOMA; TYPE B1                           0                            15
  THYMOMA; TYPE B2                           1                            29
  THYMOMA; TYPE B3                           2                            10
  THYMOMA; TYPE C                            0                            11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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(XP11.22) MUTATED       0                         0     3
  AMP PEAK 6(XP11.22) WILD-TYPE    13                         6    99
D6V7, multiclass
                           clus
vv                          AMP PEAK 6(XP11.22) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               3
                           clus
vv                          AMP PEAK 6(XP11.22) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
                               cls
clus                             0  1
  AMP PEAK 6(XP11.22) MUTATED    0  3
  AMP PEAK 6(XP11.22) WILD-TYPE  9 97
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(XP11.22) MUTATED      0    3
  AMP PEAK 6(XP11.22) WILD-TYPE    9   97
                        clus
vv                       AMP PEAK 6(XP11.22) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       AMP PEAK 6(XP11.22) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                            97
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK 7(XQ23) MUTATION ANALYSIS
D7V1, survival
                            sevent
clus2                          0   1
  AMP PEAK 7(XQ23) MUTATED     4   3
  AMP PEAK 7(XQ23) WILD-TYPE 109   6
  AMP PEAK 7(XQ23) MUTATED AMP PEAK 7(XQ23) WILD-TYPE 
                         7                        115 
  AMP PEAK 7(XQ23) MUTATED AMP PEAK 7(XQ23) WILD-TYPE 
                         3                          6 
$`AMP PEAK 7(XQ23) MUTATED`
TCGA-XM-AAZ1 TCGA-3G-AB0T TCGA-3G-AB14 TCGA-4V-A9QR TCGA-X7-A8M3 TCGA-XU-A931 
       13.05        81.80        25.48        25.64         1.64        52.90 
TCGA-ZB-A96F 
       57.90 

$`AMP PEAK 7(XQ23) WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XU-A92Q 
       95.67        23.57        15.09        50.83        12.69        35.90 
TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O TCGA-3G-AB0Q 
       25.48        26.83        71.11        45.63        68.58        59.15 
TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ 
       15.35        21.14        18.77        34.52        96.53        93.67 
TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QS TCGA-4V-A9QT 
       62.73        41.19        31.89        51.68        25.45        26.73 
TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC 
       20.61        20.71        14.27        21.99        12.89        68.12 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5V-A9RR 
       49.41        27.45        34.65        23.47        22.59        27.19 
TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD 
      138.90        10.68         1.91        65.49        59.11        36.62 
TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 
       32.25        29.62        22.85        23.18         9.50        14.50 
TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 
       42.15       125.19        54.08       150.41        64.83        83.28 
TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RE 
       40.11        52.54        48.92        37.61        97.41        13.87 
TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       26.20        11.93        12.72        84.23        32.25        37.81 
TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W 
      112.11        90.05        45.24       149.98         4.08       107.80 
TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A932 TCGA-XU-A933 
       77.03       114.67       120.43        82.65        70.65        58.82 
TCGA-XU-A936 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 
       21.14       123.68        89.46        62.17        50.53        49.38 
TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 
      107.44        24.66        35.18        49.78        23.38         5.92 
TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A 
       54.15        48.72        42.31        12.46        34.39        77.39 
TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I 
       72.69        64.44        59.80        52.80        49.45        54.35 
TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R 
       50.27         0.46        34.52        24.76        22.19        59.31 
TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       30.64        28.04        26.93        38.30        16.34        68.91 
TCGA-ZT-A8OM 
       45.96 

  AMP PEAK 7(XQ23) MUTATED AMP PEAK 7(XQ23) WILD-TYPE 
                      1.64                       0.46 
  AMP PEAK 7(XQ23) MUTATED AMP PEAK 7(XQ23) WILD-TYPE 
                     81.80                     150.41 
  AMP PEAK 7(XQ23) MUTATED AMP PEAK 7(XQ23) WILD-TYPE 
                     25.64                      41.19 
[1] "1.6 - 81.8 (25.6)"  "0.5 - 150.4 (41.2)"
[1] "hr=" "14" 
D7V2, continuous
D7V3, binary
                            cls
clus                          0  1
  AMP PEAK 7(XQ23) MUTATED    2  5
  AMP PEAK 7(XQ23) WILD-TYPE 25 91
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 7(XQ23) MUTATED      2    5
  AMP PEAK 7(XQ23) WILD-TYPE   25   91
                      clus
vv                     AMP PEAK 7(XQ23) MUTATED AMP PEAK 7(XQ23) WILD-TYPE
  ANTERIOR MEDIASTINUM                        2                         25
  THYMUS                                      5                         91
[1] 2 2
[1] FALSE
D7V4, binary
                            cls
clus                          0  1
  AMP PEAK 7(XQ23) MUTATED    3  4
  AMP PEAK 7(XQ23) WILD-TYPE 56 60
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 7(XQ23) MUTATED      3    4
  AMP PEAK 7(XQ23) WILD-TYPE   56   60
        clus
vv       AMP PEAK 7(XQ23) MUTATED AMP PEAK 7(XQ23) WILD-TYPE
  FEMALE                        3                         56
  MALE                          4                         60
[1] 2 2
[1] FALSE
D7V5, binary
                            cls
clus                          0  1
  AMP PEAK 7(XQ23) MUTATED    3  4
  AMP PEAK 7(XQ23) WILD-TYPE 78 38
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 7(XQ23) MUTATED      3    4
  AMP PEAK 7(XQ23) WILD-TYPE   78   38
     clus
vv    AMP PEAK 7(XQ23) MUTATED AMP PEAK 7(XQ23) WILD-TYPE
  NO                         3                         78
  YES                        4                         38
[1] 2 2
[1] FALSE
                            vv
clus                         THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  AMP PEAK 7(XQ23) MUTATED                 0                1                1
  AMP PEAK 7(XQ23) WILD-TYPE              17               37               14
                            vv
clus                         THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  AMP PEAK 7(XQ23) MUTATED                  2                3               0
  AMP PEAK 7(XQ23) WILD-TYPE               28                9              11
D7V6, multiclass
                  clus
vv                 AMP PEAK 7(XQ23) MUTATED AMP PEAK 7(XQ23) WILD-TYPE
  THYMOMA; TYPE A                         0                         17
  THYMOMA; TYPE AB                        1                         37
  THYMOMA; TYPE B1                        1                         14
  THYMOMA; TYPE B2                        2                         28
  THYMOMA; TYPE B3                        3                          9
  THYMOMA; TYPE C                         0                         11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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(XQ23) MUTATED       0                         0     7
  AMP PEAK 7(XQ23) WILD-TYPE    13                         6    95
D7V7, multiclass
                           clus
vv                          AMP PEAK 7(XQ23) MUTATED AMP PEAK 7(XQ23) WILD-TYPE
  ASIAN                                            0                         13
  BLACK OR AFRICAN AMERICAN                        0                          6
  WHITE                                            7                         95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                            cls
clus                          0  1
  AMP PEAK 7(XQ23) MUTATED    0  6
  AMP PEAK 7(XQ23) WILD-TYPE  9 94
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 7(XQ23) MUTATED      0    6
  AMP PEAK 7(XQ23) WILD-TYPE    9   94
                        clus
vv                       AMP PEAK 7(XQ23) MUTATED AMP PEAK 7(XQ23) WILD-TYPE
  HISPANIC OR LATINO                            0                          9
  NOT HISPANIC OR LATINO                        6                         94
[1] 2 2
[1] FALSE

Clustering(8) Variable = DEL PEAK  1(2Q37.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  1(2Q37.1) MUTATED     5   0
  DEL PEAK  1(2Q37.1) WILD-TYPE 108   9
  DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE 
                            5                           117 
  DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE 
                            0                             9 
$`DEL PEAK  1(2Q37.1) MUTATED`
TCGA-ZB-A96C TCGA-5K-AAAP TCGA-5U-AB0D TCGA-XM-AAZ2 TCGA-ZC-AAAA 
       71.11        34.65        23.47        32.25        26.93 

$`DEL PEAK  1(2Q37.1) WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XM-AAZ1 
       95.67        23.57        15.09        50.83        12.69        13.05 
TCGA-XU-A92Q TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96K TCGA-3G-AB0O TCGA-3G-AB0Q 
       35.90        25.48        26.83        45.63        68.58        59.15 
TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L 
       81.80        25.48        15.35        21.14        18.77        34.52 
TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ 
       96.53        93.67        62.73        41.19        31.89        51.68 
TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       25.64        25.45        26.73        20.61        20.71        14.27 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5U-AB0E 
       21.99        12.89        68.12        49.41        27.45        22.59 
TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC 
       27.19       138.90        10.68         1.91        65.49        59.11 
TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ 
       36.62        32.25        29.62        22.85        23.18         9.50 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 
       14.50        42.15         1.64       125.19        54.08       150.41 
TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       64.83        83.28        40.11        52.54        48.92        37.61 
TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL 
       97.41        13.87        26.20        11.93        12.72        84.23 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
       37.81       112.11        90.05        45.24       149.98         4.08 
TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 
      107.80        77.03       114.67       120.43        82.65        52.90 
TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY 
       70.65        58.82        21.14       123.68        89.46        62.17 
TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95G 
       50.53        49.38       107.44        24.66        35.18        49.78 
TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A966 
       23.38         5.92        54.15        48.72        42.31        12.46 
TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F 
       34.39        77.39        72.69        64.44        59.80        57.90 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O 
       52.80        49.45        54.35        50.27         0.46        34.52 
TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAF 
       24.76        22.19        59.31        30.64        28.04        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       16.34        68.91        45.96 

  DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE 
                        23.47                          0.46 
  DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE 
                        71.11                        150.41 
  DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE 
                        32.25                         42.15 
[1] "23.5 - 71.1 (32.2)" "0.5 - 150.4 (42.1)"
[1] "hr="     "2.6e+07"
D8V2, continuous
D8V3, binary
                               cls
clus                             0  1
  DEL PEAK  1(2Q37.1) MUTATED    3  2
  DEL PEAK  1(2Q37.1) WILD-TYPE 24 94
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(2Q37.1) MUTATED      3    2
  DEL PEAK  1(2Q37.1) WILD-TYPE   24   94
                      clus
vv                     DEL PEAK  1(2Q37.1) MUTATED
  ANTERIOR MEDIASTINUM                           3
  THYMUS                                         2
                      clus
vv                     DEL PEAK  1(2Q37.1) WILD-TYPE
  ANTERIOR MEDIASTINUM                            24
  THYMUS                                          94
[1] 2 2
[1] FALSE
D8V4, binary
                               cls
clus                             0  1
  DEL PEAK  1(2Q37.1) MUTATED    2  3
  DEL PEAK  1(2Q37.1) WILD-TYPE 57 61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(2Q37.1) MUTATED      2    3
  DEL PEAK  1(2Q37.1) WILD-TYPE   57   61
        clus
vv       DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE
  FEMALE                           2                            57
  MALE                             3                            61
[1] 2 2
[1] FALSE
D8V5, binary
                               cls
clus                             0  1
  DEL PEAK  1(2Q37.1) MUTATED    4  1
  DEL PEAK  1(2Q37.1) WILD-TYPE 77 41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(2Q37.1) MUTATED      4    1
  DEL PEAK  1(2Q37.1) WILD-TYPE   77   41
     clus
vv    DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE
  NO                            4                            77
  YES                           1                            41
[1] 2 2
[1] FALSE
                               vv
clus                            THYMOMA; TYPE A THYMOMA; TYPE AB
  DEL PEAK  1(2Q37.1) MUTATED                 2                1
  DEL PEAK  1(2Q37.1) WILD-TYPE              15               37
                               vv
clus                            THYMOMA; TYPE B1 THYMOMA; TYPE B2
  DEL PEAK  1(2Q37.1) MUTATED                  0                1
  DEL PEAK  1(2Q37.1) WILD-TYPE               15               29
                               vv
clus                            THYMOMA; TYPE B3 THYMOMA; TYPE C
  DEL PEAK  1(2Q37.1) MUTATED                  0               1
  DEL PEAK  1(2Q37.1) WILD-TYPE               12              10
D8V6, multiclass
                  clus
vv                 DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE
  THYMOMA; TYPE A                            2                            15
  THYMOMA; TYPE AB                           1                            37
  THYMOMA; TYPE B1                           0                            15
  THYMOMA; TYPE B2                           1                            29
  THYMOMA; TYPE B3                           0                            12
  THYMOMA; TYPE C                            1                            10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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(2Q37.1) MUTATED       0                         1     4
  DEL PEAK  1(2Q37.1) WILD-TYPE    13                         5    98
D8V7, multiclass
                           clus
vv                          DEL PEAK  1(2Q37.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                               4
                           clus
vv                          DEL PEAK  1(2Q37.1) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                               cls
clus                             0  1
  DEL PEAK  1(2Q37.1) MUTATED    3  2
  DEL PEAK  1(2Q37.1) WILD-TYPE  6 98
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(2Q37.1) MUTATED      3    2
  DEL PEAK  1(2Q37.1) WILD-TYPE    6   98
                        clus
vv                       DEL PEAK  1(2Q37.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                           2
                        clus
vv                       DEL PEAK  1(2Q37.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            98
[1] 2 2
[1] FALSE

Clustering(9) Variable = DEL PEAK  2(3P22.2) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(3P22.2) MUTATED    12   2
  DEL PEAK  2(3P22.2) WILD-TYPE 101   7
  DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE 
                           14                           108 
  DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE 
                            2                             7 
$`DEL PEAK  2(3P22.2) MUTATED`
TCGA-3G-AB14 TCGA-3S-A8YW TCGA-4V-A9QN TCGA-4X-A9FD TCGA-5U-AB0E TCGA-XM-A8RC 
       25.48        21.14        31.89        49.41        22.59        97.41 
TCGA-XU-A92X TCGA-XU-A930 TCGA-YT-A95G TCGA-ZB-A966 TCGA-ZB-A96I TCGA-ZB-A96L 
       77.03        82.65        49.78        12.46        54.35        50.27 
TCGA-ZC-AAAA TCGA-ZC-AAAF 
       26.93        38.30 

$`DEL PEAK  2(3P22.2) WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XM-AAZ1 
       95.67        23.57        15.09        50.83        12.69        13.05 
TCGA-XU-A92Q TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O 
       35.90        25.48        26.83        71.11        45.63        68.58 
TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI 
       59.15        81.80        15.35        18.77        34.52        96.53 
TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS 
       93.67        62.73        41.19        51.68        25.64        25.45 
TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA 
       26.73        20.61        20.71        14.27        21.99        12.89 
TCGA-4X-A9FC TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5V-A9RR TCGA-X7-A8D6 
       68.12        27.45        34.65        23.47        27.19       138.90 
TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE 
       10.68         1.91        65.49        59.11        36.62        32.25 
TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 
       29.62        22.85        23.18         9.50        14.50        42.15 
TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 
        1.64       125.19        54.08       150.41        64.83        83.28 
TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF 
       40.11        52.54        48.92        37.61        13.87        26.20 
TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O 
       11.93        12.72        84.23        32.25        37.81       112.11 
TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92Y 
       90.05        45.24       149.98         4.08       107.80       114.67 
TCGA-XU-A92Z TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXW 
      120.43        52.90        70.65        58.82        21.14       123.68 
TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D 
       89.46        62.17        50.53        49.38       107.44        24.66 
TCGA-YT-A95E TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 
       35.18        23.38         5.92        54.15        48.72        42.31 
TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F 
       34.39        77.39        72.69        64.44        59.80        57.90 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
       52.80        49.45         0.46        34.52        24.76        22.19 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       59.31        30.64        28.04        16.34        68.91        45.96 

  DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE 
                        12.46                          0.46 
  DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE 
                        97.41                        150.41 
  DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE 
                       43.855                        40.650 
[1] "12.5 - 97.4 (43.9)" "0.5 - 150.4 (40.6)"
[1] "hr=" "2.7"
D9V2, continuous
D9V3, binary
                               cls
clus                             0  1
  DEL PEAK  2(3P22.2) MUTATED    5  9
  DEL PEAK  2(3P22.2) WILD-TYPE 22 87
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(3P22.2) MUTATED      5    9
  DEL PEAK  2(3P22.2) WILD-TYPE   22   87
                      clus
vv                     DEL PEAK  2(3P22.2) MUTATED
  ANTERIOR MEDIASTINUM                           5
  THYMUS                                         9
                      clus
vv                     DEL PEAK  2(3P22.2) WILD-TYPE
  ANTERIOR MEDIASTINUM                            22
  THYMUS                                          87
[1] 2 2
[1] FALSE
D9V4, binary
                               cls
clus                             0  1
  DEL PEAK  2(3P22.2) MUTATED    7  7
  DEL PEAK  2(3P22.2) WILD-TYPE 52 57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(3P22.2) MUTATED      7    7
  DEL PEAK  2(3P22.2) WILD-TYPE   52   57
        clus
vv       DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE
  FEMALE                           7                            52
  MALE                             7                            57
[1] 2 2
[1] FALSE
D9V5, binary
                               cls
clus                             0  1
  DEL PEAK  2(3P22.2) MUTATED    8  6
  DEL PEAK  2(3P22.2) WILD-TYPE 73 36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(3P22.2) MUTATED      8    6
  DEL PEAK  2(3P22.2) WILD-TYPE   73   36
     clus
vv    DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE
  NO                            8                            73
  YES                           6                            36
[1] 2 2
[1] FALSE
                               vv
clus                            THYMOMA; TYPE A THYMOMA; TYPE AB
  DEL PEAK  2(3P22.2) MUTATED                 0                2
  DEL PEAK  2(3P22.2) WILD-TYPE              17               36
                               vv
clus                            THYMOMA; TYPE B1 THYMOMA; TYPE B2
  DEL PEAK  2(3P22.2) MUTATED                  0                6
  DEL PEAK  2(3P22.2) WILD-TYPE               15               24
                               vv
clus                            THYMOMA; TYPE B3 THYMOMA; TYPE C
  DEL PEAK  2(3P22.2) MUTATED                  4               2
  DEL PEAK  2(3P22.2) WILD-TYPE                8               9
D9V6, multiclass
                  clus
vv                 DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE
  THYMOMA; TYPE A                            0                            17
  THYMOMA; TYPE AB                           2                            36
  THYMOMA; TYPE B1                           0                            15
  THYMOMA; TYPE B2                           6                            24
  THYMOMA; TYPE B3                           4                             8
  THYMOMA; TYPE C                            2                             9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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(3P22.2) MUTATED       1                         0    13
  DEL PEAK  2(3P22.2) WILD-TYPE    12                         6    89
D9V7, multiclass
                           clus
vv                          DEL PEAK  2(3P22.2) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              13
                           clus
vv                          DEL PEAK  2(3P22.2) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                               cls
clus                             0  1
  DEL PEAK  2(3P22.2) MUTATED    4  9
  DEL PEAK  2(3P22.2) WILD-TYPE  5 91
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(3P22.2) MUTATED      4    9
  DEL PEAK  2(3P22.2) WILD-TYPE    5   91
                        clus
vv                       DEL PEAK  2(3P22.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                           9
                        clus
vv                       DEL PEAK  2(3P22.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            91
[1] 2 2
[1] FALSE

Clustering(10) Variable = DEL PEAK  3(6P25.2) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  3(6P25.2) MUTATED   20  5
  DEL PEAK  3(6P25.2) WILD-TYPE 93  4
  DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE 
                           25                            97 
  DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE 
                            5                             4 
$`DEL PEAK  3(6P25.2) MUTATED`
TCGA-XM-A8RD TCGA-3G-AB14 TCGA-3S-A8YW TCGA-4V-A9QN TCGA-4V-A9QR TCGA-4V-A9QW 
       50.83        25.48        21.14        31.89        25.64        20.71 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-5U-AB0E TCGA-XM-A8RC TCGA-XM-AAZ2 
       49.41        27.45        23.47        22.59        97.41        32.25 
TCGA-XU-A92R TCGA-XU-A92V TCGA-XU-A92X TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 
       90.05         4.08        77.03       120.43        82.65        52.90 
TCGA-XU-A932 TCGA-XU-A936 TCGA-YT-A95G TCGA-ZB-A961 TCGA-ZB-A96F TCGA-ZC-AAA7 
       70.65        21.14        49.78         5.92        57.90        28.04 
TCGA-ZC-AAAA 
       26.93 

$`DEL PEAK  3(6P25.2) WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RG TCGA-XM-AAZ1 TCGA-XU-A92Q 
       95.67        23.57        15.09        12.69        13.05        35.90 
TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O TCGA-3G-AB0Q 
       25.48        26.83        71.11        45.63        68.58        59.15 
TCGA-3G-AB0T TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ 
       81.80        15.35        18.77        34.52        96.53        93.67 
TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       62.73        41.19        51.68        25.45        26.73        20.61 
TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-5K-AAAP TCGA-5V-A9RR 
       14.27        21.99        12.89        68.12        34.65        27.19 
TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD 
      138.90        10.68         1.91        65.49        59.11        36.62 
TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 
       32.25        29.62        22.85        23.18         9.50        14.50 
TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 
       42.15         1.64       125.19        54.08       150.41        64.83 
TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE 
       83.28        40.11        52.54        48.92        37.61        13.87 
TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ3 TCGA-XU-A92O 
       26.20        11.93        12.72        84.23        37.81       112.11 
TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92W TCGA-XU-A92Y TCGA-XU-A933 TCGA-XU-AAXW 
       45.24       149.98       107.80       114.67        58.82       123.68 
TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D 
       89.46        62.17        50.53        49.38       107.44        24.66 
TCGA-YT-A95E TCGA-YT-A95H TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A966 
       35.18        23.38        54.15        48.72        42.31        12.46 
TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G 
       34.39        77.39        72.69        64.44        59.80        52.80 
TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
       49.45        54.35        50.27         0.46        34.52        24.76 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       22.19        59.31        30.64        38.30        16.34        68.91 
TCGA-ZT-A8OM 
       45.96 

  DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE 
                         4.08                          0.46 
  DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE 
                       120.43                        150.41 
  DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE 
                        31.89                         42.15 
[1] "4.1 - 120.4 (31.9)" "0.5 - 150.4 (42.1)"
[1] "hr=" "5.5"
D10V2, continuous
D10V3, binary
                               cls
clus                             0  1
  DEL PEAK  3(6P25.2) MUTATED    6 20
  DEL PEAK  3(6P25.2) WILD-TYPE 21 76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(6P25.2) MUTATED      6   20
  DEL PEAK  3(6P25.2) WILD-TYPE   21   76
                      clus
vv                     DEL PEAK  3(6P25.2) MUTATED
  ANTERIOR MEDIASTINUM                           6
  THYMUS                                        20
                      clus
vv                     DEL PEAK  3(6P25.2) WILD-TYPE
  ANTERIOR MEDIASTINUM                            21
  THYMUS                                          76
[1] 2 2
[1] FALSE
D10V4, binary
                               cls
clus                             0  1
  DEL PEAK  3(6P25.2) MUTATED   12 14
  DEL PEAK  3(6P25.2) WILD-TYPE 47 50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(6P25.2) MUTATED     12   14
  DEL PEAK  3(6P25.2) WILD-TYPE   47   50
        clus
vv       DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE
  FEMALE                          12                            47
  MALE                            14                            50
[1] 2 2
[1] FALSE
D10V5, binary
                               cls
clus                             0  1
  DEL PEAK  3(6P25.2) MUTATED   16 10
  DEL PEAK  3(6P25.2) WILD-TYPE 65 32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(6P25.2) MUTATED     16   10
  DEL PEAK  3(6P25.2) WILD-TYPE   65   32
     clus
vv    DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE
  NO                           16                            65
  YES                          10                            32
[1] 2 2
[1] FALSE
                               vv
clus                            THYMOMA; TYPE A THYMOMA; TYPE AB
  DEL PEAK  3(6P25.2) MUTATED                 2                5
  DEL PEAK  3(6P25.2) WILD-TYPE              15               33
                               vv
clus                            THYMOMA; TYPE B1 THYMOMA; TYPE B2
  DEL PEAK  3(6P25.2) MUTATED                  0                8
  DEL PEAK  3(6P25.2) WILD-TYPE               15               22
                               vv
clus                            THYMOMA; TYPE B3 THYMOMA; TYPE C
  DEL PEAK  3(6P25.2) MUTATED                  5               6
  DEL PEAK  3(6P25.2) WILD-TYPE                7               5
D10V6, multiclass
                  clus
vv                 DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE
  THYMOMA; TYPE A                            2                            15
  THYMOMA; TYPE AB                           5                            33
  THYMOMA; TYPE B1                           0                            15
  THYMOMA; TYPE B2                           8                            22
  THYMOMA; TYPE B3                           5                             7
  THYMOMA; TYPE C                            6                             5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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(6P25.2) MUTATED       5                         1    20
  DEL PEAK  3(6P25.2) WILD-TYPE     8                         5    82
D10V7, multiclass
                           clus
vv                          DEL PEAK  3(6P25.2) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              20
                           clus
vv                          DEL PEAK  3(6P25.2) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                               cls
clus                             0  1
  DEL PEAK  3(6P25.2) MUTATED    5 19
  DEL PEAK  3(6P25.2) WILD-TYPE  4 81
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(6P25.2) MUTATED      5   19
  DEL PEAK  3(6P25.2) WILD-TYPE    4   81
                        clus
vv                       DEL PEAK  3(6P25.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          19
                        clus
vv                       DEL PEAK  3(6P25.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            81
[1] 2 2
[1] FALSE

Clustering(11) Variable = DEL PEAK  4(6Q21) MUTATION ANALYSIS
D11V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  4(6Q21) MUTATED   17  3
  DEL PEAK  4(6Q21) WILD-TYPE 96  6
  DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE 
                         20                         102 
  DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE 
                          3                           6 
$`DEL PEAK  4(6Q21) MUTATED`
TCGA-XM-A8RD TCGA-3G-AB14 TCGA-3S-A8YW TCGA-4V-A9QN TCGA-4V-A9QR TCGA-4X-A9FD 
       50.83        25.48        21.14        31.89        25.64        49.41 
TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-5U-AB0E TCGA-X7-A8M0 TCGA-XM-A8RC TCGA-XU-A92X 
       27.45        23.47        22.59        14.50        97.41        77.03 
TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A936 TCGA-YT-A95G TCGA-ZB-A96F TCGA-ZB-A96I 
       82.65        52.90        21.14        49.78        57.90        54.35 
TCGA-ZC-AAA7 TCGA-ZC-AAAA 
       28.04        26.93 

$`DEL PEAK  4(6Q21) WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RG TCGA-XM-AAZ1 TCGA-XU-A92Q 
       95.67        23.57        15.09        12.69        13.05        35.90 
TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O TCGA-3G-AB0Q 
       25.48        26.83        71.11        45.63        68.58        59.15 
TCGA-3G-AB0T TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ 
       81.80        15.35        18.77        34.52        96.53        93.67 
TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       62.73        41.19        51.68        25.45        26.73        20.61 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-5K-AAAP 
       20.71        14.27        21.99        12.89        68.12        34.65 
TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC 
       27.19       138.90        10.68         1.91        65.49        59.11 
TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ 
       36.62        32.25        29.62        22.85        23.18         9.50 
TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 
       42.15         1.64       125.19        54.08       150.41        64.83 
TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE 
       83.28        40.11        52.54        48.92        37.61        13.87 
TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       26.20        11.93        12.72        84.23        32.25        37.81 
TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W 
      112.11        90.05        45.24       149.98         4.08       107.80 
TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-AAXW TCGA-XU-AAXX 
      114.67       120.43        70.65        58.82       123.68        89.46 
TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E 
       62.17        50.53        49.38       107.44        24.66        35.18 
TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A966 
       23.38         5.92        54.15        48.72        42.31        12.46 
TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G 
       34.39        77.39        72.69        64.44        59.80        52.80 
TCGA-ZB-A96H TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
       49.45        50.27         0.46        34.52        24.76        22.19 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       59.31        30.64        38.30        16.34        68.91        45.96 

  DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE 
                      14.50                        0.46 
  DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE 
                      97.41                      150.41 
  DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE 
                     29.965                      41.670 
[1] "14.5 - 97.4 (30.0)" "0.5 - 150.4 (41.7)"
[1] "hr=" "3.7"
D11V2, continuous
D11V3, binary
                             cls
clus                           0  1
  DEL PEAK  4(6Q21) MUTATED    6 14
  DEL PEAK  4(6Q21) WILD-TYPE 21 82
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(6Q21) MUTATED      6   14
  DEL PEAK  4(6Q21) WILD-TYPE   21   82
                      clus
vv                     DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE
  ANTERIOR MEDIASTINUM                         6                          21
  THYMUS                                      14                          82
[1] 2 2
[1] FALSE
D11V4, binary
                             cls
clus                           0  1
  DEL PEAK  4(6Q21) MUTATED   11  9
  DEL PEAK  4(6Q21) WILD-TYPE 48 55
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(6Q21) MUTATED     11    9
  DEL PEAK  4(6Q21) WILD-TYPE   48   55
        clus
vv       DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE
  FEMALE                        11                          48
  MALE                           9                          55
[1] 2 2
[1] FALSE
D11V5, binary
                             cls
clus                           0  1
  DEL PEAK  4(6Q21) MUTATED   12  8
  DEL PEAK  4(6Q21) WILD-TYPE 69 34
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(6Q21) MUTATED     12    8
  DEL PEAK  4(6Q21) WILD-TYPE   69   34
     clus
vv    DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE
  NO                         12                          69
  YES                         8                          34
[1] 2 2
[1] FALSE
                             vv
clus                          THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1
  DEL PEAK  4(6Q21) MUTATED                 0                2                0
  DEL PEAK  4(6Q21) WILD-TYPE              17               36               15
                             vv
clus                          THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
  DEL PEAK  4(6Q21) MUTATED                  8                5               5
  DEL PEAK  4(6Q21) WILD-TYPE               22                7               6
D11V6, multiclass
                  clus
vv                 DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE
  THYMOMA; TYPE A                          0                          17
  THYMOMA; TYPE AB                         2                          36
  THYMOMA; TYPE B1                         0                          15
  THYMOMA; TYPE B2                         8                          22
  THYMOMA; TYPE B3                         5                           7
  THYMOMA; TYPE C                          5                           6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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(6Q21) MUTATED       1                         0    19
  DEL PEAK  4(6Q21) WILD-TYPE    12                         6    83
D11V7, multiclass
                           clus
vv                          DEL PEAK  4(6Q21) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            19
                           clus
vv                          DEL PEAK  4(6Q21) WILD-TYPE
  ASIAN                                              12
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
                             cls
clus                           0  1
  DEL PEAK  4(6Q21) MUTATED    5 13
  DEL PEAK  4(6Q21) WILD-TYPE  4 87
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(6Q21) MUTATED      5   13
  DEL PEAK  4(6Q21) WILD-TYPE    4   87
                        clus
vv                       DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE
  HISPANIC OR LATINO                             5                           4
  NOT HISPANIC OR LATINO                        13                          87
[1] 2 2
[1] FALSE

Clustering(12) Variable = DEL PEAK  5(7Q36.3) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(7Q36.3) MUTATED     3   0
  DEL PEAK  5(7Q36.3) WILD-TYPE 110   9
  DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE 
                            3                           119 
  DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE 
                            0                             9 
$`DEL PEAK  5(7Q36.3) MUTATED`
TCGA-3S-A8YW TCGA-X7-A8M0 TCGA-XU-A936 
       21.14        14.50        21.14 

$`DEL PEAK  5(7Q36.3) WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XM-AAZ1 
       95.67        23.57        15.09        50.83        12.69        13.05 
TCGA-XU-A92Q TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O 
       35.90        25.48        26.83        71.11        45.63        68.58 
TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L 
       59.15        81.80        25.48        15.35        18.77        34.52 
TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ 
       96.53        93.67        62.73        41.19        31.89        51.68 
TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       25.64        25.45        26.73        20.61        20.71        14.27 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP 
       21.99        12.89        68.12        49.41        27.45        34.65 
TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 
       23.47        22.59        27.19       138.90        10.68         1.91 
TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG 
       65.49        59.11        36.62        32.25        29.62        22.85 
TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 
       23.18         9.50        42.15         1.64       125.19        54.08 
TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
      150.41        64.83        83.28        40.11        52.54        48.92 
TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI 
       37.61        97.41        13.87        26.20        11.93        12.72 
TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T 
       84.23        32.25        37.81       112.11        90.05        45.24 
TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A92Z 
      149.98         4.08       107.80        77.03       114.67       120.43 
TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-AAXW TCGA-XU-AAXX 
       82.65        52.90        70.65        58.82       123.68        89.46 
TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E 
       62.17        50.53        49.38       107.44        24.66        35.18 
TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 
       49.78        23.38         5.92        54.15        48.72        42.31 
TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E 
       12.46        34.39        77.39        72.69        64.44        59.80 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M 
       57.90        52.80        49.45        54.35        50.27         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 
       34.52        24.76        22.19        59.31        30.64        28.04 
TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       26.93        38.30        16.34        68.91        45.96 

  DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE 
                        14.50                          0.46 
  DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE 
                        21.14                        150.41 
  DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE 
                        21.14                         42.15 
[1] "14.5 - 21.1 (21.1)" "0.5 - 150.4 (42.1)"
[1] "hr="     "9300000"
D12V2, continuous
D12V3, binary
                               cls
clus                             0  1
  DEL PEAK  5(7Q36.3) MUTATED    1  2
  DEL PEAK  5(7Q36.3) WILD-TYPE 26 94
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(7Q36.3) MUTATED      1    2
  DEL PEAK  5(7Q36.3) WILD-TYPE   26   94
                      clus
vv                     DEL PEAK  5(7Q36.3) MUTATED
  ANTERIOR MEDIASTINUM                           1
  THYMUS                                         2
                      clus
vv                     DEL PEAK  5(7Q36.3) WILD-TYPE
  ANTERIOR MEDIASTINUM                            26
  THYMUS                                          94
[1] 2 2
[1] FALSE
D12V4, binary
                               cls
clus                             0  1
  DEL PEAK  5(7Q36.3) MUTATED    2  1
  DEL PEAK  5(7Q36.3) WILD-TYPE 57 63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(7Q36.3) MUTATED      2    1
  DEL PEAK  5(7Q36.3) WILD-TYPE   57   63
        clus
vv       DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE
  FEMALE                           2                            57
  MALE                             1                            63
[1] 2 2
[1] FALSE
D12V5, binary
                               cls
clus                             0  1
  DEL PEAK  5(7Q36.3) MUTATED    1  2
  DEL PEAK  5(7Q36.3) WILD-TYPE 80 40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(7Q36.3) MUTATED      1    2
  DEL PEAK  5(7Q36.3) WILD-TYPE   80   40
     clus
vv    DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE
  NO                            1                            80
  YES                           2                            40
[1] 2 2
[1] FALSE
                               vv
clus                            THYMOMA; TYPE A THYMOMA; TYPE AB
  DEL PEAK  5(7Q36.3) MUTATED                 0                0
  DEL PEAK  5(7Q36.3) WILD-TYPE              17               38
                               vv
clus                            THYMOMA; TYPE B1 THYMOMA; TYPE B2
  DEL PEAK  5(7Q36.3) MUTATED                  0                1
  DEL PEAK  5(7Q36.3) WILD-TYPE               15               29
                               vv
clus                            THYMOMA; TYPE B3 THYMOMA; TYPE C
  DEL PEAK  5(7Q36.3) MUTATED                  0               2
  DEL PEAK  5(7Q36.3) WILD-TYPE               12               9
D12V6, multiclass
                  clus
vv                 DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE
  THYMOMA; TYPE A                            0                            17
  THYMOMA; TYPE AB                           0                            38
  THYMOMA; TYPE B1                           0                            15
  THYMOMA; TYPE B2                           1                            29
  THYMOMA; TYPE B3                           0                            12
  THYMOMA; TYPE C                            2                             9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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(7Q36.3) MUTATED       0                         0     3
  DEL PEAK  5(7Q36.3) WILD-TYPE    13                         6    99
D12V7, multiclass
                           clus
vv                          DEL PEAK  5(7Q36.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               3
                           clus
vv                          DEL PEAK  5(7Q36.3) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                               cls
clus                             0  1
  DEL PEAK  5(7Q36.3) MUTATED    1  2
  DEL PEAK  5(7Q36.3) WILD-TYPE  8 98
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(7Q36.3) MUTATED      1    2
  DEL PEAK  5(7Q36.3) WILD-TYPE    8   98
                        clus
vv                       DEL PEAK  5(7Q36.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           2
                        clus
vv                       DEL PEAK  5(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                            98
[1] 2 2
[1] FALSE

Clustering(13) Variable = DEL PEAK  6(9P22.1) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(9P22.1) MUTATED     6   0
  DEL PEAK  6(9P22.1) WILD-TYPE 107   9
  DEL PEAK  6(9P22.1) MUTATED DEL PEAK  6(9P22.1) WILD-TYPE 
                            6                           116 
  DEL PEAK  6(9P22.1) MUTATED DEL PEAK  6(9P22.1) WILD-TYPE 
                            0                             9 
$`DEL PEAK  6(9P22.1) MUTATED`
TCGA-3S-A8YW TCGA-5U-AB0D TCGA-XU-A936 TCGA-ZB-A962 TCGA-ZB-A969 TCGA-ZB-A96L 
       21.14        23.47        21.14        54.15        34.39        50.27 

$`DEL PEAK  6(9P22.1) WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XM-AAZ1 
       95.67        23.57        15.09        50.83        12.69        13.05 
TCGA-XU-A92Q TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O 
       35.90        25.48        26.83        71.11        45.63        68.58 
TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L 
       59.15        81.80        25.48        15.35        18.77        34.52 
TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ 
       96.53        93.67        62.73        41.19        31.89        51.68 
TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       25.64        25.45        26.73        20.61        20.71        14.27 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP 
       21.99        12.89        68.12        49.41        27.45        34.65 
TCGA-5U-AB0E TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB 
       22.59        27.19       138.90        10.68         1.91        65.49 
TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI 
       59.11        36.62        32.25        29.62        22.85        23.18 
TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 
        9.50        14.50        42.15         1.64       125.19        54.08 
TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
      150.41        64.83        83.28        40.11        52.54        48.92 
TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI 
       37.61        97.41        13.87        26.20        11.93        12.72 
TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T 
       84.23        32.25        37.81       112.11        90.05        45.24 
TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A92Z 
      149.98         4.08       107.80        77.03       114.67       120.43 
TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-AAXW TCGA-XU-AAXX 
       82.65        52.90        70.65        58.82       123.68        89.46 
TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E 
       62.17        50.53        49.38       107.44        24.66        35.18 
TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A966 
       49.78        23.38         5.92        48.72        42.31        12.46 
TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G 
       77.39        72.69        64.44        59.80        57.90        52.80 
TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
       49.45        54.35         0.46        34.52        24.76        22.19 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
       59.31        30.64        28.04        26.93        38.30        16.34 
TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       68.91        45.96 

  DEL PEAK  6(9P22.1) MUTATED DEL PEAK  6(9P22.1) WILD-TYPE 
                        21.14                          0.46 
  DEL PEAK  6(9P22.1) MUTATED DEL PEAK  6(9P22.1) WILD-TYPE 
                        54.15                        150.41 
  DEL PEAK  6(9P22.1) MUTATED DEL PEAK  6(9P22.1) WILD-TYPE 
                        28.93                         41.67 
[1] "21.1 - 54.1 (28.9)" "0.5 - 150.4 (41.7)"
[1] "hr="     "2.6e+07"
D13V2, continuous
D13V3, binary
                               cls
clus                             0  1
  DEL PEAK  6(9P22.1) MUTATED    3  3
  DEL PEAK  6(9P22.1) WILD-TYPE 24 93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(9P22.1) MUTATED      3    3
  DEL PEAK  6(9P22.1) WILD-TYPE   24   93
                      clus
vv                     DEL PEAK  6(9P22.1) MUTATED
  ANTERIOR MEDIASTINUM                           3
  THYMUS                                         3
                      clus
vv                     DEL PEAK  6(9P22.1) WILD-TYPE
  ANTERIOR MEDIASTINUM                            24
  THYMUS                                          93
[1] 2 2
[1] FALSE
D13V4, binary
                               cls
clus                             0  1
  DEL PEAK  6(9P22.1) MUTATED    4  2
  DEL PEAK  6(9P22.1) WILD-TYPE 55 62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(9P22.1) MUTATED      4    2
  DEL PEAK  6(9P22.1) WILD-TYPE   55   62
        clus
vv       DEL PEAK  6(9P22.1) MUTATED DEL PEAK  6(9P22.1) WILD-TYPE
  FEMALE                           4                            55
  MALE                             2                            62
[1] 2 2
[1] FALSE
D13V5, binary
                               cls
clus                             0  1
  DEL PEAK  6(9P22.1) MUTATED    3  3
  DEL PEAK  6(9P22.1) WILD-TYPE 78 39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(9P22.1) MUTATED      3    3
  DEL PEAK  6(9P22.1) WILD-TYPE   78   39
     clus
vv    DEL PEAK  6(9P22.1) MUTATED DEL PEAK  6(9P22.1) WILD-TYPE
  NO                            3                            78
  YES                           3                            39
[1] 2 2
[1] FALSE
                               vv
clus                            THYMOMA; TYPE A THYMOMA; TYPE AB
  DEL PEAK  6(9P22.1) MUTATED                 1                0
  DEL PEAK  6(9P22.1) WILD-TYPE              16               38
                               vv
clus                            THYMOMA; TYPE B1 THYMOMA; TYPE B2
  DEL PEAK  6(9P22.1) MUTATED                  0                0
  DEL PEAK  6(9P22.1) WILD-TYPE               15               30
                               vv
clus                            THYMOMA; TYPE B3 THYMOMA; TYPE C
  DEL PEAK  6(9P22.1) MUTATED                  1               4
  DEL PEAK  6(9P22.1) WILD-TYPE               11               7
D13V6, multiclass
                  clus
vv                 DEL PEAK  6(9P22.1) MUTATED DEL PEAK  6(9P22.1) WILD-TYPE
  THYMOMA; TYPE A                            1                            16
  THYMOMA; TYPE AB                           0                            38
  THYMOMA; TYPE B1                           0                            15
  THYMOMA; TYPE B2                           0                            30
  THYMOMA; TYPE B3                           1                            11
  THYMOMA; TYPE C                            4                             7
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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(9P22.1) MUTATED       0                         0     6
  DEL PEAK  6(9P22.1) WILD-TYPE    13                         6    96
D13V7, multiclass
                           clus
vv                          DEL PEAK  6(9P22.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               6
                           clus
vv                          DEL PEAK  6(9P22.1) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
                               cls
clus                             0  1
  DEL PEAK  6(9P22.1) MUTATED    2  4
  DEL PEAK  6(9P22.1) WILD-TYPE  7 96
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(9P22.1) MUTATED      2    4
  DEL PEAK  6(9P22.1) WILD-TYPE    7   96
                        clus
vv                       DEL PEAK  6(9P22.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                           4
                        clus
vv                       DEL PEAK  6(9P22.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            96
[1] 2 2
[1] FALSE

Clustering(14) Variable = DEL PEAK  7(9P21.3) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(9P21.3) MUTATED    10   1
  DEL PEAK  7(9P21.3) WILD-TYPE 103   8
  DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE 
                           11                           111 
  DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE 
                            1                             8 
$`DEL PEAK  7(9P21.3) MUTATED`
TCGA-3S-A8YW TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-X7-A8M3 TCGA-XU-A92R TCGA-XU-A936 
       21.14        27.45        23.47         1.64        90.05        21.14 
TCGA-ZB-A962 TCGA-ZB-A969 TCGA-ZB-A96L TCGA-ZB-A96V TCGA-ZC-AAA7 
       54.15        34.39        50.27        30.64        28.04 

$`DEL PEAK  7(9P21.3) WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XM-AAZ1 
       95.67        23.57        15.09        50.83        12.69        13.05 
TCGA-XU-A92Q TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O 
       35.90        25.48        26.83        71.11        45.63        68.58 
TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L 
       59.15        81.80        25.48        15.35        18.77        34.52 
TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ 
       96.53        93.67        62.73        41.19        31.89        51.68 
TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       25.64        25.45        26.73        20.61        20.71        14.27 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5K-AAAP TCGA-5U-AB0E 
       21.99        12.89        68.12        49.41        34.65        22.59 
TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC 
       27.19       138.90        10.68         1.91        65.49        59.11 
TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ 
       36.62        32.25        29.62        22.85        23.18         9.50 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 
       14.50        42.15       125.19        54.08       150.41        64.83 
TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC 
       83.28        40.11        52.54        48.92        37.61        97.41 
TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ2 
       13.87        26.20        11.93        12.72        84.23        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W 
       37.81       112.11        45.24       149.98         4.08       107.80 
TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 
       77.03       114.67       120.43        82.65        52.90        70.65 
TCGA-XU-A933 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 
       58.82       123.68        89.46        62.17        50.53        49.38 
TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 
      107.44        24.66        35.18        49.78        23.38         5.92 
TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D 
       48.72        42.31        12.46        77.39        72.69        64.44 
TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96M 
       59.80        57.90        52.80        49.45        54.35         0.46 
TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZC-AAAA TCGA-ZC-AAAF 
       34.52        24.76        22.19        59.31        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       16.34        68.91        45.96 

  DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE 
                         1.64                          0.46 
  DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE 
                        90.05                        150.41 
  DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE 
                        28.04                         42.31 
[1] "1.6 - 90.0 (28.0)"  "0.5 - 150.4 (42.3)"
[1] "hr=" "2.1"
D14V2, continuous
D14V3, binary
                               cls
clus                             0  1
  DEL PEAK  7(9P21.3) MUTATED    3  8
  DEL PEAK  7(9P21.3) WILD-TYPE 24 88
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(9P21.3) MUTATED      3    8
  DEL PEAK  7(9P21.3) WILD-TYPE   24   88
                      clus
vv                     DEL PEAK  7(9P21.3) MUTATED
  ANTERIOR MEDIASTINUM                           3
  THYMUS                                         8
                      clus
vv                     DEL PEAK  7(9P21.3) WILD-TYPE
  ANTERIOR MEDIASTINUM                            24
  THYMUS                                          88
[1] 2 2
[1] FALSE
D14V4, binary
                               cls
clus                             0  1
  DEL PEAK  7(9P21.3) MUTATED    7  4
  DEL PEAK  7(9P21.3) WILD-TYPE 52 60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(9P21.3) MUTATED      7    4
  DEL PEAK  7(9P21.3) WILD-TYPE   52   60
        clus
vv       DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE
  FEMALE                           7                            52
  MALE                             4                            60
[1] 2 2
[1] FALSE
D14V5, binary
                               cls
clus                             0  1
  DEL PEAK  7(9P21.3) MUTATED    7  4
  DEL PEAK  7(9P21.3) WILD-TYPE 74 38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(9P21.3) MUTATED      7    4
  DEL PEAK  7(9P21.3) WILD-TYPE   74   38
     clus
vv    DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE
  NO                            7                            74
  YES                           4                            38
[1] 2 2
[1] FALSE
                               vv
clus                            THYMOMA; TYPE A THYMOMA; TYPE AB
  DEL PEAK  7(9P21.3) MUTATED                 1                1
  DEL PEAK  7(9P21.3) WILD-TYPE              16               37
                               vv
clus                            THYMOMA; TYPE B1 THYMOMA; TYPE B2
  DEL PEAK  7(9P21.3) MUTATED                  0                0
  DEL PEAK  7(9P21.3) WILD-TYPE               15               30
                               vv
clus                            THYMOMA; TYPE B3 THYMOMA; TYPE C
  DEL PEAK  7(9P21.3) MUTATED                  2               7
  DEL PEAK  7(9P21.3) WILD-TYPE               10               4
D14V6, multiclass
                  clus
vv                 DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE
  THYMOMA; TYPE A                            1                            16
  THYMOMA; TYPE AB                           1                            37
  THYMOMA; TYPE B1                           0                            15
  THYMOMA; TYPE B2                           0                            30
  THYMOMA; TYPE B3                           2                            10
  THYMOMA; TYPE C                            7                             4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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(9P21.3) MUTATED       1                         0    10
  DEL PEAK  7(9P21.3) WILD-TYPE    12                         6    92
D14V7, multiclass
                           clus
vv                          DEL PEAK  7(9P21.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              10
                           clus
vv                          DEL PEAK  7(9P21.3) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, binary
                               cls
clus                             0  1
  DEL PEAK  7(9P21.3) MUTATED    2  9
  DEL PEAK  7(9P21.3) WILD-TYPE  7 91
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(9P21.3) MUTATED      2    9
  DEL PEAK  7(9P21.3) WILD-TYPE    7   91
                        clus
vv                       DEL PEAK  7(9P21.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                           9
                        clus
vv                       DEL PEAK  7(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            91
[1] 2 2
[1] FALSE

Clustering(15) Variable = DEL PEAK  8(10Q26.3) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  8(10Q26.3) MUTATED     5   1
  DEL PEAK  8(10Q26.3) WILD-TYPE 108   8
  DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE 
                             6                            116 
  DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE 
                             1                              8 
$`DEL PEAK  8(10Q26.3) MUTATED`
TCGA-XM-A8RG TCGA-4V-A9QN TCGA-X7-A8M0 TCGA-XU-A92V TCGA-XU-A930 TCGA-ZB-A969 
       12.69        31.89        14.50         4.08        82.65        34.39 

$`DEL PEAK  8(10Q26.3) WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-AAZ1 TCGA-XU-A92Q 
       95.67        23.57        15.09        50.83        13.05        35.90 
TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O TCGA-3G-AB0Q 
       25.48        26.83        71.11        45.63        68.58        59.15 
TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L 
       81.80        25.48        15.35        21.14        18.77        34.52 
TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QR 
       96.53        93.67        62.73        41.19        51.68        25.64 
TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 
       25.45        26.73        20.61        20.71        14.27        21.99 
TCGA-4X-A9FA TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D 
       12.89        68.12        49.41        27.45        34.65        23.47 
TCGA-5U-AB0E TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB 
       22.59        27.19       138.90        10.68         1.91        65.49 
TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI 
       59.11        36.62        32.25        29.62        22.85        23.18 
TCGA-X7-A8DJ TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 
        9.50        42.15         1.64       125.19        54.08       150.41 
TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       64.83        83.28        40.11        52.54        48.92        37.61 
TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL 
       97.41        13.87        26.20        11.93        12.72        84.23 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U 
       32.25        37.81       112.11        90.05        45.24       149.98 
TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A931 TCGA-XU-A932 
      107.80        77.03       114.67       120.43        52.90        70.65 
TCGA-XU-A933 TCGA-XU-A936 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ 
       58.82        21.14       123.68        89.46        62.17        50.53 
TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95G TCGA-YT-A95H 
       49.38       107.44        24.66        35.18        49.78        23.38 
TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A96A 
        5.92        54.15        48.72        42.31        12.46        77.39 
TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H 
       72.69        64.44        59.80        57.90        52.80        49.45 
TCGA-ZB-A96I TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
       54.35        50.27         0.46        34.52        24.76        22.19 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH 
       59.31        30.64        28.04        26.93        38.30        16.34 
TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       68.91        45.96 

  DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE 
                          4.08                           0.46 
  DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE 
                         82.65                         150.41 
  DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE 
                        23.195                         42.230 
[1] "4.1 - 82.7 (23.2)"  "0.5 - 150.4 (42.2)"
[1] "hr=" "4"  
D15V2, continuous
D15V3, binary
                                cls
clus                              0  1
  DEL PEAK  8(10Q26.3) MUTATED    1  5
  DEL PEAK  8(10Q26.3) WILD-TYPE 26 91
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(10Q26.3) MUTATED      1    5
  DEL PEAK  8(10Q26.3) WILD-TYPE   26   91
                      clus
vv                     DEL PEAK  8(10Q26.3) MUTATED
  ANTERIOR MEDIASTINUM                            1
  THYMUS                                          5
                      clus
vv                     DEL PEAK  8(10Q26.3) WILD-TYPE
  ANTERIOR MEDIASTINUM                             26
  THYMUS                                           91
[1] 2 2
[1] FALSE
D15V4, binary
                                cls
clus                              0  1
  DEL PEAK  8(10Q26.3) MUTATED    4  2
  DEL PEAK  8(10Q26.3) WILD-TYPE 55 62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(10Q26.3) MUTATED      4    2
  DEL PEAK  8(10Q26.3) WILD-TYPE   55   62
        clus
vv       DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE
  FEMALE                            4                             55
  MALE                              2                             62
[1] 2 2
[1] FALSE
D15V5, binary
                                cls
clus                              0  1
  DEL PEAK  8(10Q26.3) MUTATED    4  2
  DEL PEAK  8(10Q26.3) WILD-TYPE 77 40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(10Q26.3) MUTATED      4    2
  DEL PEAK  8(10Q26.3) WILD-TYPE   77   40
     clus
vv    DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE
  NO                             4                             77
  YES                            2                             40
[1] 2 2
[1] FALSE
                                vv
clus                             THYMOMA; TYPE A THYMOMA; TYPE AB
  DEL PEAK  8(10Q26.3) MUTATED                 1                1
  DEL PEAK  8(10Q26.3) WILD-TYPE              16               37
                                vv
clus                             THYMOMA; TYPE B1 THYMOMA; TYPE B2
  DEL PEAK  8(10Q26.3) MUTATED                  0                1
  DEL PEAK  8(10Q26.3) WILD-TYPE               15               29
                                vv
clus                             THYMOMA; TYPE B3 THYMOMA; TYPE C
  DEL PEAK  8(10Q26.3) MUTATED                  2               1
  DEL PEAK  8(10Q26.3) WILD-TYPE               10              10
D15V6, multiclass
                  clus
vv                 DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE
  THYMOMA; TYPE A                             1                             16
  THYMOMA; TYPE AB                            1                             37
  THYMOMA; TYPE B1                            0                             15
  THYMOMA; TYPE B2                            1                             29
  THYMOMA; TYPE B3                            2                             10
  THYMOMA; TYPE C                             1                             10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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(10Q26.3) MUTATED       1                         0     5
  DEL PEAK  8(10Q26.3) WILD-TYPE    12                         6    97
D15V7, multiclass
                           clus
vv                          DEL PEAK  8(10Q26.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                5
                           clus
vv                          DEL PEAK  8(10Q26.3) WILD-TYPE
  ASIAN                                                 12
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                                cls
clus                              0  1
  DEL PEAK  8(10Q26.3) MUTATED    1  5
  DEL PEAK  8(10Q26.3) WILD-TYPE  8 95
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(10Q26.3) MUTATED      1    5
  DEL PEAK  8(10Q26.3) WILD-TYPE    8   95
                        clus
vv                       DEL PEAK  8(10Q26.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            5
                        clus
vv                       DEL PEAK  8(10Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                             95
[1] 2 2
[1] FALSE

Clustering(16) Variable = DEL PEAK  9(19P13.11) MUTATION ANALYSIS
D16V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK  9(19P13.11) MUTATED     5   0
  DEL PEAK  9(19P13.11) WILD-TYPE 108   9
  DEL PEAK  9(19P13.11) MUTATED DEL PEAK  9(19P13.11) WILD-TYPE 
                              5                             117 
  DEL PEAK  9(19P13.11) MUTATED DEL PEAK  9(19P13.11) WILD-TYPE 
                              0                               9 
$`DEL PEAK  9(19P13.11) MUTATED`
TCGA-3S-A8YW TCGA-5U-AB0D TCGA-XU-A936 TCGA-ZB-A969 TCGA-ZB-A96L 
       21.14        23.47        21.14        34.39        50.27 

$`DEL PEAK  9(19P13.11) WILD-TYPE`
TCGA-3G-AB19 TCGA-4X-A9FB TCGA-5U-AB0F TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XM-AAZ1 
       95.67        23.57        15.09        50.83        12.69        13.05 
TCGA-XU-A92Q TCGA-YT-A95F TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O 
       35.90        25.48        26.83        71.11        45.63        68.58 
TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L 
       59.15        81.80        25.48        15.35        18.77        34.52 
TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ 
       96.53        93.67        62.73        41.19        31.89        51.68 
TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       25.64        25.45        26.73        20.61        20.71        14.27 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP 
       21.99        12.89        68.12        49.41        27.45        34.65 
TCGA-5U-AB0E TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB 
       22.59        27.19       138.90        10.68         1.91        65.49 
TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI 
       59.11        36.62        32.25        29.62        22.85        23.18 
TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 
        9.50        14.50        42.15         1.64       125.19        54.08 
TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
      150.41        64.83        83.28        40.11        52.54        48.92 
TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI 
       37.61        97.41        13.87        26.20        11.93        12.72 
TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T 
       84.23        32.25        37.81       112.11        90.05        45.24 
TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A92Z 
      149.98         4.08       107.80        77.03       114.67       120.43 
TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-AAXW TCGA-XU-AAXX 
       82.65        52.90        70.65        58.82       123.68        89.46 
TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E 
       62.17        50.53        49.38       107.44        24.66        35.18 
TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 
       49.78        23.38         5.92        54.15        48.72        42.31 
TCGA-ZB-A966 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F 
       12.46        77.39        72.69        64.44        59.80        57.90 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
       52.80        49.45        54.35         0.46        34.52        24.76 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF 
       22.19        59.31        30.64        28.04        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 TCGA-ZT-A8OM 
       16.34        68.91        45.96 

  DEL PEAK  9(19P13.11) MUTATED DEL PEAK  9(19P13.11) WILD-TYPE 
                          21.14                            0.46 
  DEL PEAK  9(19P13.11) MUTATED DEL PEAK  9(19P13.11) WILD-TYPE 
                          50.27                          150.41 
  DEL PEAK  9(19P13.11) MUTATED DEL PEAK  9(19P13.11) WILD-TYPE 
                          23.47                           42.15 
[1] "21.1 - 50.3 (23.5)" "0.5 - 150.4 (42.1)"
[1] "hr="     "9400000"
D16V2, continuous
D16V3, binary
                                 cls
clus                               0  1
  DEL PEAK  9(19P13.11) MUTATED    3  2
  DEL PEAK  9(19P13.11) WILD-TYPE 24 94
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK  9(19P13.11) MUTATED      3    2
  DEL PEAK  9(19P13.11) WILD-TYPE   24   94
                      clus
vv                     DEL PEAK  9(19P13.11) MUTATED
  ANTERIOR MEDIASTINUM                             3
  THYMUS                                           2
                      clus
vv                     DEL PEAK  9(19P13.11) WILD-TYPE
  ANTERIOR MEDIASTINUM                              24
  THYMUS                                            94
[1] 2 2
[1] FALSE
D16V4, binary
                                 cls
clus                               0  1
  DEL PEAK  9(19P13.11) MUTATED    4  1
  DEL PEAK  9(19P13.11) WILD-TYPE 55 63
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK  9(19P13.11) MUTATED      4    1
  DEL PEAK  9(19P13.11) WILD-TYPE   55   63
        clus
vv       DEL PEAK  9(19P13.11) MUTATED DEL PEAK  9(19P13.11) WILD-TYPE
  FEMALE                             4                              55
  MALE                               1                              63
[1] 2 2
[1] FALSE
D16V5, binary
                                 cls
clus                               0  1
  DEL PEAK  9(19P13.11) MUTATED    3  2
  DEL PEAK  9(19P13.11) WILD-TYPE 78 40
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK  9(19P13.11) MUTATED      3    2
  DEL PEAK  9(19P13.11) WILD-TYPE   78   40
     clus
vv    DEL PEAK  9(19P13.11) MUTATED DEL PEAK  9(19P13.11) WILD-TYPE
  NO                              3                              78
  YES                             2                              40
[1] 2 2
[1] FALSE
                                 vv
clus                              THYMOMA; TYPE A THYMOMA; TYPE AB
  DEL PEAK  9(19P13.11) MUTATED                 0                0
  DEL PEAK  9(19P13.11) WILD-TYPE              17               38
                                 vv
clus                              THYMOMA; TYPE B1 THYMOMA; TYPE B2
  DEL PEAK  9(19P13.11) MUTATED                  0                0
  DEL PEAK  9(19P13.11) WILD-TYPE               15               30
                                 vv
clus                              THYMOMA; TYPE B3 THYMOMA; TYPE C
  DEL PEAK  9(19P13.11) MUTATED                  1               4
  DEL PEAK  9(19P13.11) WILD-TYPE               11               7
D16V6, multiclass
                  clus
vv                 DEL PEAK  9(19P13.11) MUTATED
  THYMOMA; TYPE A                              0
  THYMOMA; TYPE AB                             0
  THYMOMA; TYPE B1                             0
  THYMOMA; TYPE B2                             0
  THYMOMA; TYPE B3                             1
  THYMOMA; TYPE C                              4
                  clus
vv                 DEL PEAK  9(19P13.11) WILD-TYPE
  THYMOMA; TYPE A                               17
  THYMOMA; TYPE AB                              38
  THYMOMA; TYPE B1                              15
  THYMOMA; TYPE B2                              30
  THYMOMA; TYPE B3                              11
  THYMOMA; TYPE C                                7
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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(19P13.11) MUTATED       0                         0     5
  DEL PEAK  9(19P13.11) WILD-TYPE    13                         6    97
D16V7, multiclass
                           clus
vv                          DEL PEAK  9(19P13.11) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                 5
                           clus
vv                          DEL PEAK  9(19P13.11) WILD-TYPE
  ASIAN                                                  13
  BLACK OR AFRICAN AMERICAN                               6
  WHITE                                                  97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                                 cls
clus                               0  1
  DEL PEAK  9(19P13.11) MUTATED    2  3
  DEL PEAK  9(19P13.11) WILD-TYPE  7 97
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK  9(19P13.11) MUTATED      2    3
  DEL PEAK  9(19P13.11) WILD-TYPE    7   97
                        clus
vv                       DEL PEAK  9(19P13.11) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                             3
                        clus
vv                       DEL PEAK  9(19P13.11) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                              97
[1] 2 2
[1] FALSE

Clustering(17) Variable = DEL PEAK 10(22Q12.1) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 10(22Q12.1) MUTATED   16  2
  DEL PEAK 10(22Q12.1) WILD-TYPE 97  7
  DEL PEAK 10(22Q12.1) MUTATED DEL PEAK 10(22Q12.1) WILD-TYPE 
                            18                            104 
  DEL PEAK 10(22Q12.1) MUTATED DEL PEAK 10(22Q12.1) WILD-TYPE 
                             2                              7 
$`DEL PEAK 10(22Q12.1) MUTATED`
TCGA-3G-AB19 TCGA-5U-AB0F TCGA-ZB-A96K TCGA-3S-A8YW TCGA-4V-A9QJ TCGA-4V-A9QN 
       95.67        15.09        45.63        21.14        93.67        31.89 
TCGA-4V-A9QX TCGA-5K-AAAP TCGA-5U-AB0D TCGA-XM-A8RC TCGA-XM-A8RF TCGA-XM-AAZ2 
       14.27        34.65        23.47        97.41        26.20        32.25 
TCGA-XU-A92V TCGA-XU-A936 TCGA-ZB-A963 TCGA-ZB-A96A TCGA-ZB-A96L TCGA-ZT-A8OM 
        4.08        21.14        48.72        77.39        50.27        45.96 

$`DEL PEAK 10(22Q12.1) WILD-TYPE`
TCGA-4X-A9FB TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XM-AAZ1 TCGA-XU-A92Q TCGA-YT-A95F 
       23.57        50.83        12.69        13.05        35.90        25.48 
TCGA-ZB-A965 TCGA-ZB-A96C TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 
       26.83        71.11        68.58        59.15        81.80        25.48 
TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QL TCGA-4V-A9QM 
       15.35        18.77        34.52        96.53        62.73        41.19 
TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW 
       51.68        25.64        25.45        26.73        20.61        20.71 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5U-AB0E 
       21.99        12.89        68.12        49.41        27.45        22.59 
TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 TCGA-X7-A8DB TCGA-X7-A8DC 
       27.19       138.90        10.68         1.91        65.49        59.11 
TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ 
       36.62        32.25        29.62        22.85        23.18         9.50 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M6 
       14.50        42.15         1.64       125.19        54.08       150.41 
TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       64.83        83.28        40.11        52.54        48.92        37.61 
TCGA-XM-A8RE TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ3 TCGA-XU-A92O 
       13.87        11.93        12.72        84.23        37.81       112.11 
TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y 
       90.05        45.24       149.98       107.80        77.03       114.67 
TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-AAXW 
      120.43        82.65        52.90        70.65        58.82       123.68 
TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D 
       89.46        62.17        50.53        49.38       107.44        24.66 
TCGA-YT-A95E TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A964 
       35.18        49.78        23.38         5.92        54.15        42.31 
TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96B TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F 
       12.46        34.39        72.69        64.44        59.80        57.90 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
       52.80        49.45        54.35         0.46        34.52        24.76 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF 
       22.19        59.31        30.64        28.04        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 
       16.34        68.91 

  DEL PEAK 10(22Q12.1) MUTATED DEL PEAK 10(22Q12.1) WILD-TYPE 
                          4.08                           0.46 
  DEL PEAK 10(22Q12.1) MUTATED DEL PEAK 10(22Q12.1) WILD-TYPE 
                         97.41                         150.41 
  DEL PEAK 10(22Q12.1) MUTATED DEL PEAK 10(22Q12.1) WILD-TYPE 
                         33.45                          41.67 
[1] "4.1 - 97.4 (33.5)"  "0.5 - 150.4 (41.7)"
[1] "hr=" "2.1"
D17V2, continuous
D17V3, binary
                                cls
clus                              0  1
  DEL PEAK 10(22Q12.1) MUTATED    7 12
  DEL PEAK 10(22Q12.1) WILD-TYPE 20 84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(22Q12.1) MUTATED      7   12
  DEL PEAK 10(22Q12.1) WILD-TYPE   20   84
                      clus
vv                     DEL PEAK 10(22Q12.1) MUTATED
  ANTERIOR MEDIASTINUM                            7
  THYMUS                                         12
                      clus
vv                     DEL PEAK 10(22Q12.1) WILD-TYPE
  ANTERIOR MEDIASTINUM                             20
  THYMUS                                           84
[1] 2 2
[1] FALSE
D17V4, binary
                                cls
clus                              0  1
  DEL PEAK 10(22Q12.1) MUTATED   11  8
  DEL PEAK 10(22Q12.1) WILD-TYPE 48 56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(22Q12.1) MUTATED     11    8
  DEL PEAK 10(22Q12.1) WILD-TYPE   48   56
        clus
vv       DEL PEAK 10(22Q12.1) MUTATED DEL PEAK 10(22Q12.1) WILD-TYPE
  FEMALE                           11                             48
  MALE                              8                             56
[1] 2 2
[1] FALSE
D17V5, binary
                                cls
clus                              0  1
  DEL PEAK 10(22Q12.1) MUTATED   12  7
  DEL PEAK 10(22Q12.1) WILD-TYPE 69 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(22Q12.1) MUTATED     12    7
  DEL PEAK 10(22Q12.1) WILD-TYPE   69   35
     clus
vv    DEL PEAK 10(22Q12.1) MUTATED DEL PEAK 10(22Q12.1) WILD-TYPE
  NO                            12                             69
  YES                            7                             35
[1] 2 2
[1] FALSE
                                vv
clus                             THYMOMA; TYPE A THYMOMA; TYPE AB
  DEL PEAK 10(22Q12.1) MUTATED                 5                6
  DEL PEAK 10(22Q12.1) WILD-TYPE              12               32
                                vv
clus                             THYMOMA; TYPE B1 THYMOMA; TYPE B2
  DEL PEAK 10(22Q12.1) MUTATED                  0                2
  DEL PEAK 10(22Q12.1) WILD-TYPE               15               28
                                vv
clus                             THYMOMA; TYPE B3 THYMOMA; TYPE C
  DEL PEAK 10(22Q12.1) MUTATED                  3               3
  DEL PEAK 10(22Q12.1) WILD-TYPE                9               8
D17V6, multiclass
                  clus
vv                 DEL PEAK 10(22Q12.1) MUTATED DEL PEAK 10(22Q12.1) WILD-TYPE
  THYMOMA; TYPE A                             5                             12
  THYMOMA; TYPE AB                            6                             32
  THYMOMA; TYPE B1                            0                             15
  THYMOMA; TYPE B2                            2                             28
  THYMOMA; TYPE B3                            3                              9
  THYMOMA; TYPE C                             3                              8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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(22Q12.1) MUTATED       1                         1    17
  DEL PEAK 10(22Q12.1) WILD-TYPE    12                         5    85
D17V7, multiclass
                           clus
vv                          DEL PEAK 10(22Q12.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               17
                           clus
vv                          DEL PEAK 10(22Q12.1) WILD-TYPE
  ASIAN                                                 12
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, binary
                                cls
clus                              0  1
  DEL PEAK 10(22Q12.1) MUTATED    5 14
  DEL PEAK 10(22Q12.1) WILD-TYPE  4 86
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(22Q12.1) MUTATED      5   14
  DEL PEAK 10(22Q12.1) WILD-TYPE    4   86
                        clus
vv                       DEL PEAK 10(22Q12.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           14
                        clus
vv                       DEL PEAK 10(22Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             86
[1] 2 2
[1] FALSE

Clustering(18) Variable = DEL PEAK 11(22Q13.32) MUTATION ANALYSIS
D18V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 11(22Q13.32) MUTATED   14  1
  DEL PEAK 11(22Q13.32) WILD-TYPE 99  8
  DEL PEAK 11(22Q13.32) MUTATED DEL PEAK 11(22Q13.32) WILD-TYPE 
                             15                             107 
  DEL PEAK 11(22Q13.32) MUTATED DEL PEAK 11(22Q13.32) WILD-TYPE 
                              1                               8 
$`DEL PEAK 11(22Q13.32) MUTATED`
TCGA-3G-AB19 TCGA-5U-AB0F TCGA-3S-A8YW TCGA-4V-A9QJ TCGA-4V-A9QN TCGA-4V-A9QX 
       95.67        15.09        21.14        93.67        31.89        14.27 
TCGA-5U-AB0D TCGA-XM-A8RC TCGA-XU-A92Z TCGA-XU-A936 TCGA-ZB-A963 TCGA-ZB-A969 
       23.47        97.41       120.43        21.14        48.72        34.39 
TCGA-ZB-A96A TCGA-ZB-A96L TCGA-ZT-A8OM 
       77.39        50.27        45.96 

$`DEL PEAK 11(22Q13.32) WILD-TYPE`
TCGA-4X-A9FB TCGA-XM-A8RD TCGA-XM-A8RG TCGA-XM-AAZ1 TCGA-XU-A92Q TCGA-YT-A95F 
       23.57        50.83        12.69        13.05        35.90        25.48 
TCGA-ZB-A965 TCGA-ZB-A96C TCGA-ZB-A96K TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T 
       26.83        71.11        45.63        68.58        59.15        81.80 
TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QL 
       25.48        15.35        18.77        34.52        96.53        62.73 
TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       41.19        51.68        25.64        25.45        26.73        20.61 
TCGA-4V-A9QW TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ 
       20.71        21.99        12.89        68.12        49.41        27.45 
TCGA-5K-AAAP TCGA-5U-AB0E TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 
       34.65        22.59        27.19       138.90        10.68         1.91 
TCGA-X7-A8DB TCGA-X7-A8DC TCGA-X7-A8DD TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG 
       65.49        59.11        36.62        32.25        29.62        22.85 
TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 
       23.18         9.50        14.50        42.15         1.64       125.19 
TCGA-X7-A8M5 TCGA-X7-A8M6 TCGA-X7-A8M7 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
       54.08       150.41        64.83        83.28        40.11        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI 
       48.92        37.61        13.87        26.20        11.93        12.72 
TCGA-XM-A8RL TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92R TCGA-XU-A92T 
       84.23        32.25        37.81       112.11        90.05        45.24 
TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W TCGA-XU-A92X TCGA-XU-A92Y TCGA-XU-A930 
      149.98         4.08       107.80        77.03       114.67        82.65 
TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY 
       52.90        70.65        58.82       123.68        89.46        62.17 
TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95G 
       50.53        49.38       107.44        24.66        35.18        49.78 
TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A964 TCGA-ZB-A966 TCGA-ZB-A96B 
       23.38         5.92        54.15        42.31        12.46        72.69 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I 
       64.44        59.80        57.90        52.80        49.45        54.35 
TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V 
        0.46        34.52        24.76        22.19        59.31        30.64 
TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       28.04        26.93        38.30        16.34        68.91 

  DEL PEAK 11(22Q13.32) MUTATED DEL PEAK 11(22Q13.32) WILD-TYPE 
                          14.27                            0.46 
  DEL PEAK 11(22Q13.32) MUTATED DEL PEAK 11(22Q13.32) WILD-TYPE 
                         120.43                          150.41 
  DEL PEAK 11(22Q13.32) MUTATED DEL PEAK 11(22Q13.32) WILD-TYPE 
                          45.96                           40.11 
[1] "14.3 - 120.4 (46.0)" "0.5 - 150.4 (40.1)" 
[1] "hr=" "1.4"
D18V2, continuous
D18V3, binary
                                 cls
clus                               0  1
  DEL PEAK 11(22Q13.32) MUTATED    6  9
  DEL PEAK 11(22Q13.32) WILD-TYPE 21 87
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(22Q13.32) MUTATED      6    9
  DEL PEAK 11(22Q13.32) WILD-TYPE   21   87
                      clus
vv                     DEL PEAK 11(22Q13.32) MUTATED
  ANTERIOR MEDIASTINUM                             6
  THYMUS                                           9
                      clus
vv                     DEL PEAK 11(22Q13.32) WILD-TYPE
  ANTERIOR MEDIASTINUM                              21
  THYMUS                                            87
[1] 2 2
[1] FALSE
D18V4, binary
                                 cls
clus                               0  1
  DEL PEAK 11(22Q13.32) MUTATED    9  6
  DEL PEAK 11(22Q13.32) WILD-TYPE 50 58
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(22Q13.32) MUTATED      9    6
  DEL PEAK 11(22Q13.32) WILD-TYPE   50   58
        clus
vv       DEL PEAK 11(22Q13.32) MUTATED DEL PEAK 11(22Q13.32) WILD-TYPE
  FEMALE                             9                              50
  MALE                               6                              58
[1] 2 2
[1] FALSE
D18V5, binary
                                 cls
clus                               0  1
  DEL PEAK 11(22Q13.32) MUTATED    7  8
  DEL PEAK 11(22Q13.32) WILD-TYPE 74 34
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(22Q13.32) MUTATED      7    8
  DEL PEAK 11(22Q13.32) WILD-TYPE   74   34
     clus
vv    DEL PEAK 11(22Q13.32) MUTATED DEL PEAK 11(22Q13.32) WILD-TYPE
  NO                              7                              74
  YES                             8                              34
[1] 2 2
[1] FALSE
                                 vv
clus                              THYMOMA; TYPE A THYMOMA; TYPE AB
  DEL PEAK 11(22Q13.32) MUTATED                 2                3
  DEL PEAK 11(22Q13.32) WILD-TYPE              15               35
                                 vv
clus                              THYMOMA; TYPE B1 THYMOMA; TYPE B2
  DEL PEAK 11(22Q13.32) MUTATED                  0                2
  DEL PEAK 11(22Q13.32) WILD-TYPE               15               28
                                 vv
clus                              THYMOMA; TYPE B3 THYMOMA; TYPE C
  DEL PEAK 11(22Q13.32) MUTATED                  3               5
  DEL PEAK 11(22Q13.32) WILD-TYPE                9               6
D18V6, multiclass
                  clus
vv                 DEL PEAK 11(22Q13.32) MUTATED
  THYMOMA; TYPE A                              2
  THYMOMA; TYPE AB                             3
  THYMOMA; TYPE B1                             0
  THYMOMA; TYPE B2                             2
  THYMOMA; TYPE B3                             3
  THYMOMA; TYPE C                              5
                  clus
vv                 DEL PEAK 11(22Q13.32) WILD-TYPE
  THYMOMA; TYPE A                               15
  THYMOMA; TYPE AB                              35
  THYMOMA; TYPE B1                              15
  THYMOMA; TYPE B2                              28
  THYMOMA; TYPE B3                               9
  THYMOMA; TYPE C                                6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table 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(22Q13.32) MUTATED       1                         0    14
  DEL PEAK 11(22Q13.32) WILD-TYPE    12                         6    88
D18V7, multiclass
                           clus
vv                          DEL PEAK 11(22Q13.32) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                14
                           clus
vv                          DEL PEAK 11(22Q13.32) WILD-TYPE
  ASIAN                                                  12
  BLACK OR AFRICAN AMERICAN                               6
  WHITE                                                  88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                                 cls
clus                               0  1
  DEL PEAK 11(22Q13.32) MUTATED    4 11
  DEL PEAK 11(22Q13.32) WILD-TYPE  5 89
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(22Q13.32) MUTATED      4   11
  DEL PEAK 11(22Q13.32) WILD-TYPE    5   89
                        clus
vv                       DEL PEAK 11(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            11
                        clus
vv                       DEL PEAK 11(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                              89
[1] 2 2
[1] FALSE
