[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/15092844/THYM-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THYM-TP/15104465/transformed.cor.cli.txt"

nPatients in clinical file=122, in cluster file=123, common to both=121
[1]  12 121
[1] "DEL PEAK  1(2Q37.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE 
                            5                           116 
  DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE 
                            5                           116 
[1] "DEL PEAK  2(3P22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE 
                           14                           107 
  DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE 
                           14                           107 
[1] "DEL PEAK  3(6P25.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE 
                           26                            95 
  DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE 
                           26                            95 
[1] "DEL PEAK  4(6Q21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE 
                         20                         101 
  DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE 
                         20                         101 
[1] "DEL PEAK  5(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE 
                            3                           118 
  DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE 
                            3                           118 
[1] "DEL PEAK  6(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE 
                           11                           110 
  DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE 
                           11                           110 
[1] "DEL PEAK  7(9Q22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(9Q22.33) MUTATED DEL PEAK  7(9Q22.33) WILD-TYPE 
                             3                            118 
  DEL PEAK  7(9Q22.33) MUTATED DEL PEAK  7(9Q22.33) WILD-TYPE 
                             3                            118 
[1] "DEL PEAK  8(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE 
                             6                            115 
  DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE 
                             6                            115 
[1] "DEL PEAK  9(11Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(11Q22.1) MUTATED DEL PEAK  9(11Q22.1) WILD-TYPE 
                             7                            114 
  DEL PEAK  9(11Q22.1) MUTATED DEL PEAK  9(11Q22.1) WILD-TYPE 
                             7                            114 
[1] "DEL PEAK 10(19P13.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(19P13.11) MUTATED DEL PEAK 10(19P13.11) WILD-TYPE 
                              5                             116 
  DEL PEAK 10(19P13.11) MUTATED DEL PEAK 10(19P13.11) WILD-TYPE 
                              5                             116 
[1] "DEL PEAK 11(22Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(22Q12.1) MUTATED DEL PEAK 11(22Q12.1) WILD-TYPE 
                            19                            102 
  DEL PEAK 11(22Q12.1) MUTATED DEL PEAK 11(22Q12.1) WILD-TYPE 
                            19                            102 
[1] "DEL PEAK 12(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(22Q13.32) MUTATED DEL PEAK 12(22Q13.32) WILD-TYPE 
                             15                             106 
  DEL PEAK 12(22Q13.32) MUTATED DEL PEAK 12(22Q13.32) WILD-TYPE 
                             15                             106 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "NEOPLASM_DISEASESTAGE"                 
 [6] "PATHOLOGY_T_STAGE"                     
 [7] "PATHOLOGY_N_STAGE"                     
 [8] "PATHOLOGY_M_STAGE"                     
 [9] "DCC_UPLOAD_DATE"                       
[10] "GENDER"                                
[11] "RADIATION_THERAPY"                     
[12] "RADIATIONS_RADIATION_REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCH_NUMBER"                          

Input Data has 15 rows and 121 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=6,	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:'NEOPLASM_DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NEOPLASM_DISEASESTAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH_NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "BATCH_NUMBER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
[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 121 columns, 1 survival variables, and 4 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH" "GENDER"         "RACE"           "ETHNICITY"     
YEARS_TO_BIRTH, nv=48, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = DEL PEAK  1(2Q37.1) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  1(2Q37.1) MUTATED     5   0
  DEL PEAK  1(2Q37.1) WILD-TYPE 108   6
  DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE 
                            5                           114 
  DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE 
                            0                             6 
$`DEL PEAK  1(2Q37.1) MUTATED`
TCGA-5K-AAAP TCGA-5U-AB0D TCGA-XM-AAZ2 TCGA-ZB-A96C TCGA-ZC-AAAA 
       34.65        11.57        32.25        43.43        26.93 

$`DEL PEAK  1(2Q37.1) WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       13.48         9.96        34.52        89.23        88.83        56.75 
TCGA-4V-A9QM TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT 
       38.50        28.90        45.07        19.76        19.76        21.70 
TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB 
       16.60        14.07        11.24        15.78        12.89        23.57 
TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR 
       55.46        39.45        19.50        10.36        15.09        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        49.22        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         2.37        14.50 
TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 
       42.15         1.64       125.19        54.08        83.28        30.08 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE 
       52.54        48.92        37.61        97.41        50.83         7.69 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 
       26.20        12.69        11.93        12.72        84.23        13.05 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U 
       37.81       112.11        35.90        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        18.67        13.32 
TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 
       22.78        49.78        12.79         0.13         0.20        30.74 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B 
       18.58        16.57        12.46         0.66        10.68        60.33 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I 
       42.81         0.23         0.16        32.35        37.48         5.19 
TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q 
       31.50         0.30         0.46         1.81        10.68         7.17 
TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       35.34         8.52        28.04        38.30        16.34        68.91 

  DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE 
                        11.57                          0.13 
  DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE 
                        43.43                        149.98 
  DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE 
                        32.25                         30.41 
[1] "11.6 - 43.4 (32.2)" "0.1 - 150.0 (30.4)"
[1] "hr="     "2.6e+07"
D1V2, continuous
D1V3, binary
                               cls
clus                             0  1
  DEL PEAK  1(2Q37.1) MUTATED    2  3
  DEL PEAK  1(2Q37.1) WILD-TYPE 57 59
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(2Q37.1) MUTATED      2    3
  DEL PEAK  1(2Q37.1) WILD-TYPE   57   59
        clus
vv       DEL PEAK  1(2Q37.1) MUTATED DEL PEAK  1(2Q37.1) WILD-TYPE
  FEMALE                           2                            57
  MALE                             3                            59
[1] 2 2
[1] FALSE
                               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    96
D1V4, 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                                                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"
D1V5, binary
                               cls
clus                             0  1
  DEL PEAK  1(2Q37.1) MUTATED    3  2
  DEL PEAK  1(2Q37.1) WILD-TYPE  6 96
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(2Q37.1) MUTATED      3    2
  DEL PEAK  1(2Q37.1) WILD-TYPE    6   96
                        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                            96
[1] 2 2
[1] FALSE

Clustering(2) Variable = DEL PEAK  2(3P22.2) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(3P22.2) MUTATED    13   1
  DEL PEAK  2(3P22.2) WILD-TYPE 100   5
  DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE 
                           14                           105 
  DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE 
                            1                             5 
$`DEL PEAK  2(3P22.2) MUTATED`
TCGA-3G-AB14 TCGA-3S-A8YW TCGA-4V-A9QN TCGA-4X-A9FD TCGA-5U-AB0E TCGA-XM-A8RC 
       17.75        13.48        28.90        39.45        10.36        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         5.19         0.30 
TCGA-ZC-AAAA TCGA-ZC-AAAF 
       26.93        38.30 

$`DEL PEAK  2(3P22.2) WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB19 TCGA-3Q-A9WF TCGA-3S-AAYX 
       56.65        59.15        81.80        90.61        15.35         9.96 
TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QQ 
       34.52        89.23        88.83        56.75        38.50        45.07 
TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX 
       19.76        19.76        21.70        16.60        14.07        11.24 
TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-5G-A9ZZ TCGA-5K-AAAP 
       15.78        12.89        23.57        55.46        19.50        34.65 
TCGA-5U-AB0D TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 TCGA-X7-A8D7 TCGA-X7-A8D8 
       11.57        15.09        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        49.22        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         2.37        14.50        42.15         1.64       125.19 
TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB 
       54.08        83.28        30.08        52.54        48.92        37.61 
TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI 
       50.83         7.69        26.20        12.69        11.93        12.72 
TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q 
       84.23        13.05        32.25        37.81       112.11        35.90 
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        18.67 
TCGA-YT-A95E TCGA-YT-A95F TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 
       13.32        22.78        12.79         0.13         0.20        30.74 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C 
       18.58        16.57         0.66        10.68        60.33        43.43 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96K 
       42.81         0.23         0.16        32.35        37.48        31.50 
TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V 
        0.46         1.81        10.68         7.17        35.34         8.52 
TCGA-ZC-AAA7 TCGA-ZC-AAAH TCGA-ZL-A9V6 
       28.04        16.34        68.91 

  DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE 
                         0.30                          0.13 
  DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE 
                        97.41                        149.98 
  DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE 
                       27.915                        31.500 
[1] "0.3 - 97.4 (27.9)"  "0.1 - 150.0 (31.5)"
[1] "hr=" "2"  
D2V2, continuous
D2V3, binary
                               cls
clus                             0  1
  DEL PEAK  2(3P22.2) MUTATED    7  7
  DEL PEAK  2(3P22.2) WILD-TYPE 52 55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(3P22.2) MUTATED      7    7
  DEL PEAK  2(3P22.2) WILD-TYPE   52   55
        clus
vv       DEL PEAK  2(3P22.2) MUTATED DEL PEAK  2(3P22.2) WILD-TYPE
  FEMALE                           7                            52
  MALE                             7                            55
[1] 2 2
[1] FALSE
                               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    87
D2V4, 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                                                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                               cls
clus                             0  1
  DEL PEAK  2(3P22.2) MUTATED    4  9
  DEL PEAK  2(3P22.2) WILD-TYPE  5 89
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(3P22.2) MUTATED      4    9
  DEL PEAK  2(3P22.2) WILD-TYPE    5   89
                        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                            89
[1] 2 2
[1] FALSE

Clustering(3) Variable = DEL PEAK  3(6P25.2) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  3(6P25.2) MUTATED   22  3
  DEL PEAK  3(6P25.2) WILD-TYPE 91  3
  DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE 
                           25                            94 
  DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE 
                            3                             3 
$`DEL PEAK  3(6P25.2) MUTATED`
TCGA-3G-AB14 TCGA-3S-A8YW TCGA-4V-A9QN TCGA-4V-A9QR TCGA-4V-A9QW TCGA-4X-A9FD 
       17.75        13.48        28.90        19.76        14.07        39.45 
TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-5U-AB0E TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-AAZ2 
       19.50        11.57        10.36        97.41        50.83        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         0.13         0.16        28.04 
TCGA-ZC-AAAA 
       26.93 

$`DEL PEAK  3(6P25.2) WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB19 TCGA-3Q-A9WF TCGA-3S-AAYX 
       56.65        59.15        81.80        90.61        15.35         9.96 
TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QQ 
       34.52        89.23        88.83        56.75        38.50        45.07 
TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA 
       19.76        21.70        16.60        11.24        15.78        12.89 
TCGA-4X-A9FB TCGA-4X-A9FC TCGA-5K-AAAP TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 
       23.57        55.46        34.65        15.09        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        49.22        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         2.37        14.50        42.15 
TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
        1.64       125.19        54.08        83.28        30.08        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH 
       48.92        37.61         7.69        26.20        12.69        11.93 
TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q 
       12.72        84.23        13.05        37.81       112.11        35.90 
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        18.67 
TCGA-YT-A95E TCGA-YT-A95F TCGA-YT-A95H TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 
       13.32        22.78        12.79         0.20        30.74        18.58 
TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C 
       16.57        12.46         0.66        10.68        60.33        43.43 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K 
       42.81         0.23        32.35        37.48         5.19        31.50 
TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R 
        0.30         0.46         1.81        10.68         7.17        35.34 
TCGA-ZB-A96V TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
        8.52        38.30        16.34        68.91 

  DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE 
                         0.13                          0.20 
  DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE 
                       120.43                        149.98 
  DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE 
                       28.040                        31.875 
[1] "0.1 - 120.4 (28.0)" "0.2 - 150.0 (31.9)"
[1] "hr=" "3.9"
D3V2, continuous
D3V3, binary
                               cls
clus                             0  1
  DEL PEAK  3(6P25.2) MUTATED   12 14
  DEL PEAK  3(6P25.2) WILD-TYPE 47 48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(6P25.2) MUTATED     12   14
  DEL PEAK  3(6P25.2) WILD-TYPE   47   48
        clus
vv       DEL PEAK  3(6P25.2) MUTATED DEL PEAK  3(6P25.2) WILD-TYPE
  FEMALE                          12                            47
  MALE                            14                            48
[1] 2 2
[1] FALSE
                               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    80
D3V4, 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                                                80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
                               cls
clus                             0  1
  DEL PEAK  3(6P25.2) MUTATED    5 19
  DEL PEAK  3(6P25.2) WILD-TYPE  4 79
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(6P25.2) MUTATED      5   19
  DEL PEAK  3(6P25.2) WILD-TYPE    4   79
                        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                            79
[1] 2 2
[1] FALSE

Clustering(4) Variable = DEL PEAK  4(6Q21) MUTATION ANALYSIS
D4V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  4(6Q21) MUTATED   18  2
  DEL PEAK  4(6Q21) WILD-TYPE 95  4
  DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE 
                         20                          99 
  DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE 
                          2                           4 
$`DEL PEAK  4(6Q21) MUTATED`
TCGA-3G-AB14 TCGA-3S-A8YW TCGA-4V-A9QN TCGA-4V-A9QR TCGA-4X-A9FD TCGA-5G-A9ZZ 
       17.75        13.48        28.90        19.76        39.45        19.50 
TCGA-5U-AB0D TCGA-5U-AB0E TCGA-X7-A8M0 TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XU-A92X 
       11.57        10.36        14.50        97.41        50.83        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         0.16         5.19 
TCGA-ZC-AAA7 TCGA-ZC-AAAA 
       28.04        26.93 

$`DEL PEAK  4(6Q21) WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB19 TCGA-3Q-A9WF TCGA-3S-AAYX 
       56.65        59.15        81.80        90.61        15.35         9.96 
TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QQ 
       34.52        89.23        88.83        56.75        38.50        45.07 
TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 
       19.76        21.70        16.60        14.07        11.24        15.78 
TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC TCGA-5K-AAAP TCGA-5U-AB0F TCGA-5V-A9RR 
       12.89        23.57        55.46        34.65        15.09        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        49.22        36.62 
TCGA-X7-A8DE TCGA-X7-A8DF TCGA-X7-A8DG TCGA-X7-A8DI TCGA-X7-A8DJ TCGA-X7-A8M1 
       32.25        29.62        22.85        23.18         2.37        42.15 
TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
        1.64       125.19        54.08        83.28        30.08        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH 
       48.92        37.61         7.69        26.20        12.69        11.93 
TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O 
       12.72        84.23        13.05        32.25        37.81       112.11 
TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W 
       35.90        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        18.67        13.32 
TCGA-YT-A95F TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 
       22.78        12.79         0.13         0.20        30.74        18.58 
TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C 
       16.57        12.46         0.66        10.68        60.33        43.43 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96K TCGA-ZB-A96L 
       42.81         0.23        32.35        37.48        31.50         0.30 
TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V 
        0.46         1.81        10.68         7.17        35.34         8.52 
TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       38.30        16.34        68.91 

  DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE 
                       0.16                        0.13 
  DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE 
                      97.41                      149.98 
  DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE 
                     24.035                      32.250 
[1] "0.2 - 97.4 (24.0)"  "0.1 - 150.0 (32.2)"
[1] "hr=" "4"  
D4V2, continuous
D4V3, binary
                             cls
clus                           0  1
  DEL PEAK  4(6Q21) MUTATED   11  9
  DEL PEAK  4(6Q21) WILD-TYPE 48 53
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(6Q21) MUTATED     11    9
  DEL PEAK  4(6Q21) WILD-TYPE   48   53
        clus
vv       DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE
  FEMALE                        11                          48
  MALE                           9                          53
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(6Q21) MUTATED       1                         0    19
  DEL PEAK  4(6Q21) WILD-TYPE    12                         6    81
D4V4, 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                                              81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                             cls
clus                           0  1
  DEL PEAK  4(6Q21) MUTATED    5 13
  DEL PEAK  4(6Q21) WILD-TYPE  4 85
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(6Q21) MUTATED      5   13
  DEL PEAK  4(6Q21) WILD-TYPE    4   85
                        clus
vv                       DEL PEAK  4(6Q21) MUTATED DEL PEAK  4(6Q21) WILD-TYPE
  HISPANIC OR LATINO                             5                           4
  NOT HISPANIC OR LATINO                        13                          85
[1] 2 2
[1] FALSE

Clustering(5) Variable = DEL PEAK  5(7Q36.3) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(7Q36.3) MUTATED     3   0
  DEL PEAK  5(7Q36.3) WILD-TYPE 110   6
  DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE 
                            3                           116 
  DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE 
                            0                             6 
$`DEL PEAK  5(7Q36.3) MUTATED`
TCGA-3S-A8YW TCGA-X7-A8M0 TCGA-XU-A936 
       13.48        14.50        21.14 

$`DEL PEAK  5(7Q36.3) WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       28.90        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F 
       39.45        19.50        34.65        11.57        10.36        15.09 
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        49.22 
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         2.37 
TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 
       42.15         1.64       125.19        54.08        83.28        30.08 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE 
       52.54        48.92        37.61        97.41        50.83         7.69 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 
       26.20        12.69        11.93        12.72        84.23        13.05 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T 
       32.25        37.81       112.11        35.90        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        18.67        13.32 
TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 
       22.78        49.78        12.79         0.13         0.20        30.74 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B 
       18.58        16.57        12.46         0.66        10.68        60.33 
TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H 
       43.43        42.81         0.23         0.16        32.35        37.48 
TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
        5.19        31.50         0.30         0.46         1.81        10.68 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF 
        7.17        35.34         8.52        28.04        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 
       16.34        68.91 

  DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE 
                        13.48                          0.13 
  DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE 
                        21.14                        149.98 
  DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE 
                       14.500                        31.875 
[1] "13.5 - 21.1 (14.5)" "0.1 - 150.0 (31.9)"
[1] "hr="     "9300000"
D5V2, continuous
D5V3, binary
                               cls
clus                             0  1
  DEL PEAK  5(7Q36.3) MUTATED    2  1
  DEL PEAK  5(7Q36.3) WILD-TYPE 57 61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(7Q36.3) MUTATED      2    1
  DEL PEAK  5(7Q36.3) WILD-TYPE   57   61
        clus
vv       DEL PEAK  5(7Q36.3) MUTATED DEL PEAK  5(7Q36.3) WILD-TYPE
  FEMALE                           2                            57
  MALE                             1                            61
[1] 2 2
[1] FALSE
                               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    97
D5V4, 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                                                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"
D5V5, binary
                               cls
clus                             0  1
  DEL PEAK  5(7Q36.3) MUTATED    1  2
  DEL PEAK  5(7Q36.3) WILD-TYPE  8 96
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(7Q36.3) MUTATED      1    2
  DEL PEAK  5(7Q36.3) WILD-TYPE    8   96
                        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                            96
[1] 2 2
[1] FALSE

Clustering(6) Variable = DEL PEAK  6(9P21.3) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(9P21.3) MUTATED    10   1
  DEL PEAK  6(9P21.3) WILD-TYPE 103   5
  DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE 
                           11                           108 
  DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE 
                            1                             5 
$`DEL PEAK  6(9P21.3) MUTATED`
TCGA-3S-A8YW TCGA-5G-A9ZZ TCGA-5U-AB0D TCGA-X7-A8M3 TCGA-XU-A92R TCGA-XU-A936 
       13.48        19.50        11.57         1.64        90.05        21.14 
TCGA-ZB-A962 TCGA-ZB-A969 TCGA-ZB-A96L TCGA-ZB-A96V TCGA-ZC-AAA7 
        0.20         0.66         0.30         8.52        28.04 

$`DEL PEAK  6(9P21.3) WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       28.90        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-4X-A9FD TCGA-5K-AAAP TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 
       39.45        34.65        10.36        15.09        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        49.22        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         2.37        14.50        42.15 
TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 
      125.19        54.08        83.28        30.08        52.54        48.92 
TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG 
       37.61        97.41        50.83         7.69        26.20        12.69 
TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       11.93        12.72        84.23        13.05        32.25        37.81 
TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V TCGA-XU-A92W 
      112.11        35.90        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-A95F TCGA-YT-A95G TCGA-YT-A95H 
      107.44        18.67        13.32        22.78        49.78        12.79 
TCGA-ZB-A961 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A96A 
        0.13        30.74        18.58        16.57        12.46        10.68 
TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G 
       60.33        43.43        42.81         0.23         0.16        32.35 
TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
       37.48         5.19        31.50         0.46         1.81        10.68 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
        7.17        35.34        26.93        38.30        16.34        68.91 

  DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE 
                         0.20                          0.13 
  DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE 
                        90.05                        149.98 
  DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE 
                       11.570                        33.435 
[1] "0.2 - 90.0 (11.6)"  "0.1 - 150.0 (33.4)"
[1] "hr=" "5.2"
D6V2, continuous
D6V3, binary
                               cls
clus                             0  1
  DEL PEAK  6(9P21.3) MUTATED    7  4
  DEL PEAK  6(9P21.3) WILD-TYPE 52 58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(9P21.3) MUTATED      7    4
  DEL PEAK  6(9P21.3) WILD-TYPE   52   58
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  FEMALE                           7                            52
  MALE                             4                            58
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(9P21.3) MUTATED       1                         0    10
  DEL PEAK  6(9P21.3) WILD-TYPE    12                         6    90
D6V4, multiclass
                           clus
vv                          DEL PEAK  6(9P21.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              10
                           clus
vv                          DEL PEAK  6(9P21.3) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
                               cls
clus                             0  1
  DEL PEAK  6(9P21.3) MUTATED    2  9
  DEL PEAK  6(9P21.3) WILD-TYPE  7 89
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(9P21.3) MUTATED      2    9
  DEL PEAK  6(9P21.3) WILD-TYPE    7   89
                        clus
vv                       DEL PEAK  6(9P21.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                           9
                        clus
vv                       DEL PEAK  6(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            89
[1] 2 2
[1] FALSE

Clustering(7) Variable = DEL PEAK  7(9Q22.33) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  7(9Q22.33) MUTATED     3   0
  DEL PEAK  7(9Q22.33) WILD-TYPE 110   6
  DEL PEAK  7(9Q22.33) MUTATED DEL PEAK  7(9Q22.33) WILD-TYPE 
                             3                            116 
  DEL PEAK  7(9Q22.33) MUTATED DEL PEAK  7(9Q22.33) WILD-TYPE 
                             0                              6 
$`DEL PEAK  7(9Q22.33) MUTATED`
TCGA-3S-A8YW TCGA-XU-A936 TCGA-ZB-A961 
       13.48        21.14         0.13 

$`DEL PEAK  7(9Q22.33) WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       28.90        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F 
       39.45        19.50        34.65        11.57        10.36        15.09 
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        49.22 
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         2.37 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 
       14.50        42.15         1.64       125.19        54.08        83.28 
TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD 
       30.08        52.54        48.92        37.61        97.41        50.83 
TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL 
        7.69        26.20        12.69        11.93        12.72        84.23 
TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R 
       13.05        32.25        37.81       112.11        35.90        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        18.67 
TCGA-YT-A95E TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A962 TCGA-ZB-A963 
       13.32        22.78        49.78        12.79         0.20        30.74 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B 
       18.58        16.57        12.46         0.66        10.68        60.33 
TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H 
       43.43        42.81         0.23         0.16        32.35        37.48 
TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P 
        5.19        31.50         0.30         0.46         1.81        10.68 
TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF 
        7.17        35.34         8.52        28.04        26.93        38.30 
TCGA-ZC-AAAH TCGA-ZL-A9V6 
       16.34        68.91 

  DEL PEAK  7(9Q22.33) MUTATED DEL PEAK  7(9Q22.33) WILD-TYPE 
                          0.13                           0.16 
  DEL PEAK  7(9Q22.33) MUTATED DEL PEAK  7(9Q22.33) WILD-TYPE 
                         21.14                         149.98 
  DEL PEAK  7(9Q22.33) MUTATED DEL PEAK  7(9Q22.33) WILD-TYPE 
                        13.480                         31.875 
[1] "0.1 - 21.1 (13.5)"  "0.2 - 150.0 (31.9)"
[1] "hr="     "3400000"
D7V2, continuous
D7V3, binary
                                cls
clus                              0  1
  DEL PEAK  7(9Q22.33) MUTATED    1  2
  DEL PEAK  7(9Q22.33) WILD-TYPE 58 60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(9Q22.33) MUTATED      1    2
  DEL PEAK  7(9Q22.33) WILD-TYPE   58   60
        clus
vv       DEL PEAK  7(9Q22.33) MUTATED DEL PEAK  7(9Q22.33) WILD-TYPE
  FEMALE                            1                             58
  MALE                              2                             60
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(9Q22.33) MUTATED       0                         0     3
  DEL PEAK  7(9Q22.33) WILD-TYPE    13                         6    97
D7V4, multiclass
                           clus
vv                          DEL PEAK  7(9Q22.33) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                3
                           clus
vv                          DEL PEAK  7(9Q22.33) 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"
D7V5, binary
                                cls
clus                              0  1
  DEL PEAK  7(9Q22.33) MUTATED    1  2
  DEL PEAK  7(9Q22.33) WILD-TYPE  8 96
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(9Q22.33) MUTATED      1    2
  DEL PEAK  7(9Q22.33) WILD-TYPE    8   96
                        clus
vv                       DEL PEAK  7(9Q22.33) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            2
                        clus
vv                       DEL PEAK  7(9Q22.33) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                             96
[1] 2 2
[1] FALSE

Clustering(8) Variable = DEL PEAK  8(10Q26.3) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  8(10Q26.3) MUTATED     5   1
  DEL PEAK  8(10Q26.3) WILD-TYPE 108   5
  DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE 
                             6                            113 
  DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE 
                             1                              5 
$`DEL PEAK  8(10Q26.3) MUTATED`
TCGA-4V-A9QN TCGA-X7-A8M0 TCGA-XM-A8RG TCGA-XU-A92V TCGA-XU-A930 TCGA-ZB-A969 
       28.90        14.50        12.69         4.08        82.65         0.66 

$`DEL PEAK  8(10Q26.3) WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       13.48         9.96        34.52        89.23        88.83        56.75 
TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       38.50        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0E TCGA-5U-AB0F 
       39.45        19.50        34.65        11.57        10.36        15.09 
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        49.22 
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         2.37 
TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 
       42.15         1.64       125.19        54.08        83.28        30.08 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE 
       52.54        48.92        37.61        97.41        50.83         7.69 
TCGA-XM-A8RF TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 
       26.20        11.93        12.72        84.23        13.05        32.25 
TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U 
       37.81       112.11        35.90        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-A95F TCGA-YT-A95G 
       49.38       107.44        18.67        13.32        22.78        49.78 
TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 
       12.79         0.13         0.20        30.74        18.58        16.57 
TCGA-ZB-A966 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E 
       12.46        10.68        60.33        43.43        42.81         0.23 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L 
        0.16        32.35        37.48         5.19        31.50         0.30 
TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V 
        0.46         1.81        10.68         7.17        35.34         8.52 
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  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE 
                          0.66                           0.13 
  DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE 
                         82.65                         149.98 
  DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE 
                        13.595                         32.250 
[1] "0.7 - 82.7 (13.6)"  "0.1 - 150.0 (32.2)"
[1] "hr=" "5.9"
D8V2, continuous
D8V3, binary
                                cls
clus                              0  1
  DEL PEAK  8(10Q26.3) MUTATED    4  2
  DEL PEAK  8(10Q26.3) WILD-TYPE 55 60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(10Q26.3) MUTATED      4    2
  DEL PEAK  8(10Q26.3) WILD-TYPE   55   60
        clus
vv       DEL PEAK  8(10Q26.3) MUTATED DEL PEAK  8(10Q26.3) WILD-TYPE
  FEMALE                            4                             55
  MALE                              2                             60
[1] 2 2
[1] FALSE
                                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    95
D8V4, 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                                                 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"
D8V5, binary
                                cls
clus                              0  1
  DEL PEAK  8(10Q26.3) MUTATED    1  5
  DEL PEAK  8(10Q26.3) WILD-TYPE  8 93
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(10Q26.3) MUTATED      1    5
  DEL PEAK  8(10Q26.3) WILD-TYPE    8   93
                        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                             93
[1] 2 2
[1] FALSE

Clustering(9) Variable = DEL PEAK  9(11Q22.1) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  9(11Q22.1) MUTATED     7   0
  DEL PEAK  9(11Q22.1) WILD-TYPE 106   6
  DEL PEAK  9(11Q22.1) MUTATED DEL PEAK  9(11Q22.1) WILD-TYPE 
                             7                            112 
  DEL PEAK  9(11Q22.1) MUTATED DEL PEAK  9(11Q22.1) WILD-TYPE 
                             0                              6 
$`DEL PEAK  9(11Q22.1) MUTATED`
TCGA-4V-A9QN TCGA-4X-A9FD TCGA-5U-AB0E TCGA-XM-A8RC TCGA-XU-A92X TCGA-XU-A930 
       28.90        39.45        10.36        97.41        77.03        82.65 
TCGA-ZC-AAAA 
       26.93 

$`DEL PEAK  9(11Q22.1) WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-A8YW TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL 
       13.48         9.96        34.52        89.23        88.83        56.75 
TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       38.50        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0D TCGA-5U-AB0F TCGA-5V-A9RR TCGA-X7-A8D6 
       19.50        34.65        11.57        15.09        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        49.22        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         2.37        14.50        42.15 
TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 TCGA-XM-A8R8 
        1.64       125.19        54.08        83.28        30.08        52.54 
TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RF TCGA-XM-A8RG 
       48.92        37.61        50.83         7.69        26.20        12.69 
TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ2 TCGA-XM-AAZ3 
       11.93        12.72        84.23        13.05        32.25        37.81 
TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92V 
      112.11        35.90        90.05        45.24       149.98         4.08 
TCGA-XU-A92W TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 
      107.80       114.67       120.43        52.90        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-A95F TCGA-YT-A95G TCGA-YT-A95H 
      107.44        18.67        13.32        22.78        49.78        12.79 
TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 
        0.13         0.20        30.74        18.58        16.57        12.46 
TCGA-ZB-A969 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E 
        0.66        10.68        60.33        43.43        42.81         0.23 
TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96L 
        0.16        32.35        37.48         5.19        31.50         0.30 
TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V 
        0.46         1.81        10.68         7.17        35.34         8.52 
TCGA-ZC-AAA7 TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       28.04        38.30        16.34        68.91 

  DEL PEAK  9(11Q22.1) MUTATED DEL PEAK  9(11Q22.1) WILD-TYPE 
                         10.36                           0.13 
  DEL PEAK  9(11Q22.1) MUTATED DEL PEAK  9(11Q22.1) WILD-TYPE 
                         97.41                         149.98 
  DEL PEAK  9(11Q22.1) MUTATED DEL PEAK  9(11Q22.1) WILD-TYPE 
                         39.45                          30.41 
[1] "10.4 - 97.4 (39.5)" "0.1 - 150.0 (30.4)"
[1] "hr="     "7.6e+07"
D9V2, continuous
D9V3, binary
                                cls
clus                              0  1
  DEL PEAK  9(11Q22.1) MUTATED    2  5
  DEL PEAK  9(11Q22.1) WILD-TYPE 57 57
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(11Q22.1) MUTATED      2    5
  DEL PEAK  9(11Q22.1) WILD-TYPE   57   57
        clus
vv       DEL PEAK  9(11Q22.1) MUTATED DEL PEAK  9(11Q22.1) WILD-TYPE
  FEMALE                            2                             57
  MALE                              5                             57
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(11Q22.1) MUTATED       1                         0     6
  DEL PEAK  9(11Q22.1) WILD-TYPE    12                         6    94
D9V4, multiclass
                           clus
vv                          DEL PEAK  9(11Q22.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                6
                           clus
vv                          DEL PEAK  9(11Q22.1) WILD-TYPE
  ASIAN                                                 12
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
                                cls
clus                              0  1
  DEL PEAK  9(11Q22.1) MUTATED    3  4
  DEL PEAK  9(11Q22.1) WILD-TYPE  6 94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(11Q22.1) MUTATED      3    4
  DEL PEAK  9(11Q22.1) WILD-TYPE    6   94
                        clus
vv                       DEL PEAK  9(11Q22.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                            4
                        clus
vv                       DEL PEAK  9(11Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             94
[1] 2 2
[1] FALSE

Clustering(10) Variable = DEL PEAK 10(19P13.11) MUTATION ANALYSIS
D10V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 10(19P13.11) MUTATED     5   0
  DEL PEAK 10(19P13.11) WILD-TYPE 108   6
  DEL PEAK 10(19P13.11) MUTATED DEL PEAK 10(19P13.11) WILD-TYPE 
                              5                             114 
  DEL PEAK 10(19P13.11) MUTATED DEL PEAK 10(19P13.11) WILD-TYPE 
                              0                               6 
$`DEL PEAK 10(19P13.11) MUTATED`
TCGA-3S-A8YW TCGA-5U-AB0D TCGA-XU-A936 TCGA-ZB-A969 TCGA-ZB-A96L 
       13.48        11.57        21.14         0.66         0.30 

$`DEL PEAK 10(19P13.11) WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3G-AB19 TCGA-3Q-A9WF 
       56.65        59.15        81.80        17.75        90.61        15.35 
TCGA-3S-AAYX TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QJ TCGA-4V-A9QL TCGA-4V-A9QM 
        9.96        34.52        89.23        88.83        56.75        38.50 
TCGA-4V-A9QN TCGA-4V-A9QQ TCGA-4V-A9QR TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU 
       28.90        45.07        19.76        19.76        21.70        16.60 
TCGA-4V-A9QW TCGA-4V-A9QX TCGA-4X-A9F9 TCGA-4X-A9FA TCGA-4X-A9FB TCGA-4X-A9FC 
       14.07        11.24        15.78        12.89        23.57        55.46 
TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0E TCGA-5U-AB0F TCGA-5V-A9RR 
       39.45        19.50        34.65        10.36        15.09        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        49.22        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         2.37        14.50 
TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 
       42.15         1.64       125.19        54.08        83.28        30.08 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RC TCGA-XM-A8RD TCGA-XM-A8RE 
       52.54        48.92        37.61        97.41        50.83         7.69 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 
       26.20        12.69        11.93        12.72        84.23        13.05 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T 
       32.25        37.81       112.11        35.90        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        18.67        13.32 
TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A963 
       22.78        49.78        12.79         0.13         0.20        30.74 
TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A96A TCGA-ZB-A96B TCGA-ZB-A96C 
       18.58        16.57        12.46        10.68        60.33        43.43 
TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I 
       42.81         0.23         0.16        32.35        37.48         5.19 
TCGA-ZB-A96K TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R 
       31.50         0.46         1.81        10.68         7.17        35.34 
TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
        8.52        28.04        26.93        38.30        16.34        68.91 

  DEL PEAK 10(19P13.11) MUTATED DEL PEAK 10(19P13.11) WILD-TYPE 
                           0.30                            0.13 
  DEL PEAK 10(19P13.11) MUTATED DEL PEAK 10(19P13.11) WILD-TYPE 
                          21.14                          149.98 
  DEL PEAK 10(19P13.11) MUTATED DEL PEAK 10(19P13.11) WILD-TYPE 
                          11.57                           32.25 
[1] "0.3 - 21.1 (11.6)"  "0.1 - 150.0 (32.2)"
[1] "hr="     "9200000"
D10V2, continuous
D10V3, binary
                                 cls
clus                               0  1
  DEL PEAK 10(19P13.11) MUTATED    4  1
  DEL PEAK 10(19P13.11) WILD-TYPE 55 61
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 10(19P13.11) MUTATED      4    1
  DEL PEAK 10(19P13.11) WILD-TYPE   55   61
        clus
vv       DEL PEAK 10(19P13.11) MUTATED DEL PEAK 10(19P13.11) WILD-TYPE
  FEMALE                             4                              55
  MALE                               1                              61
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(19P13.11) MUTATED       0                         0     5
  DEL PEAK 10(19P13.11) WILD-TYPE    13                         6    95
D10V4, multiclass
                           clus
vv                          DEL PEAK 10(19P13.11) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                 5
                           clus
vv                          DEL PEAK 10(19P13.11) WILD-TYPE
  ASIAN                                                  13
  BLACK OR AFRICAN AMERICAN                               6
  WHITE                                                  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"
D10V5, binary
                                 cls
clus                               0  1
  DEL PEAK 10(19P13.11) MUTATED    2  3
  DEL PEAK 10(19P13.11) WILD-TYPE  7 95
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 10(19P13.11) MUTATED      2    3
  DEL PEAK 10(19P13.11) WILD-TYPE    7   95
                        clus
vv                       DEL PEAK 10(19P13.11) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                             3
                        clus
vv                       DEL PEAK 10(19P13.11) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                              95
[1] 2 2
[1] FALSE

Clustering(11) Variable = DEL PEAK 11(22Q12.1) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 11(22Q12.1) MUTATED   16  1
  DEL PEAK 11(22Q12.1) WILD-TYPE 97  5
  DEL PEAK 11(22Q12.1) MUTATED DEL PEAK 11(22Q12.1) WILD-TYPE 
                            17                            102 
  DEL PEAK 11(22Q12.1) MUTATED DEL PEAK 11(22Q12.1) WILD-TYPE 
                             1                              5 
$`DEL PEAK 11(22Q12.1) MUTATED`
TCGA-3G-AB19 TCGA-3S-A8YW TCGA-4V-A9QJ TCGA-4V-A9QN TCGA-4V-A9QX TCGA-5K-AAAP 
       90.61        13.48        88.83        28.90        11.24        34.65 
TCGA-5U-AB0D TCGA-5U-AB0F TCGA-XM-A8RC TCGA-XM-A8RF TCGA-XM-AAZ2 TCGA-XU-A92V 
       11.57        15.09        97.41        26.20        32.25         4.08 
TCGA-XU-A936 TCGA-ZB-A963 TCGA-ZB-A96A TCGA-ZB-A96K TCGA-ZB-A96L 
       21.14        30.74        10.68        31.50         0.30 

$`DEL PEAK 11(22Q12.1) WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-AAYX 
       56.65        59.15        81.80        17.75        15.35         9.96 
TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QR 
       34.52        89.23        56.75        38.50        45.07        19.76 
TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4X-A9F9 TCGA-4X-A9FA 
       19.76        21.70        16.60        14.07        15.78        12.89 
TCGA-4X-A9FB TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5U-AB0E TCGA-5V-A9RR 
       23.57        55.46        39.45        19.50        10.36        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        49.22        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         2.37        14.50 
TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 TCGA-XH-A853 
       42.15         1.64       125.19        54.08        83.28        30.08 
TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RD TCGA-XM-A8RE TCGA-XM-A8RG 
       52.54        48.92        37.61        50.83         7.69        12.69 
TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 TCGA-XM-AAZ3 TCGA-XU-A92O 
       11.93        12.72        84.23        13.05        37.81       112.11 
TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T TCGA-XU-A92U TCGA-XU-A92W TCGA-XU-A92X 
       35.90        90.05        45.24       149.98       107.80        77.03 
TCGA-XU-A92Y TCGA-XU-A92Z TCGA-XU-A930 TCGA-XU-A931 TCGA-XU-A932 TCGA-XU-A933 
      114.67       120.43        82.65        52.90        70.65        58.82 
TCGA-XU-AAXW TCGA-XU-AAXX TCGA-XU-AAXY TCGA-XU-AAXZ TCGA-XU-AAY0 TCGA-XU-AAY1 
      123.68        89.46        62.17        50.53        49.38       107.44 
TCGA-YT-A95D TCGA-YT-A95E TCGA-YT-A95F TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 
       18.67        13.32        22.78        49.78        12.79         0.13 
TCGA-ZB-A962 TCGA-ZB-A964 TCGA-ZB-A965 TCGA-ZB-A966 TCGA-ZB-A969 TCGA-ZB-A96B 
        0.20        18.58        16.57        12.46         0.66        60.33 
TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F TCGA-ZB-A96G TCGA-ZB-A96H 
       43.43        42.81         0.23         0.16        32.35        37.48 
TCGA-ZB-A96I TCGA-ZB-A96M TCGA-ZB-A96O TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R 
        5.19         0.46         1.81        10.68         7.17        35.34 
TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
        8.52        28.04        26.93        38.30        16.34        68.91 

  DEL PEAK 11(22Q12.1) MUTATED DEL PEAK 11(22Q12.1) WILD-TYPE 
                          0.30                           0.13 
  DEL PEAK 11(22Q12.1) MUTATED DEL PEAK 11(22Q12.1) WILD-TYPE 
                         97.41                         149.98 
  DEL PEAK 11(22Q12.1) MUTATED DEL PEAK 11(22Q12.1) WILD-TYPE 
                        26.200                         33.435 
[1] "0.3 - 97.4 (26.2)"  "0.1 - 150.0 (33.4)"
[1] "hr=" "1.7"
D11V2, continuous
D11V3, binary
                                cls
clus                              0  1
  DEL PEAK 11(22Q12.1) MUTATED   11  8
  DEL PEAK 11(22Q12.1) WILD-TYPE 48 54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(22Q12.1) MUTATED     11    8
  DEL PEAK 11(22Q12.1) WILD-TYPE   48   54
        clus
vv       DEL PEAK 11(22Q12.1) MUTATED DEL PEAK 11(22Q12.1) WILD-TYPE
  FEMALE                           11                             48
  MALE                              8                             54
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(22Q12.1) MUTATED       1                         1    17
  DEL PEAK 11(22Q12.1) WILD-TYPE    12                         5    83
D11V4, multiclass
                           clus
vv                          DEL PEAK 11(22Q12.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               17
                           clus
vv                          DEL PEAK 11(22Q12.1) WILD-TYPE
  ASIAN                                                 12
  BLACK OR AFRICAN AMERICAN                              5
  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"
D11V5, binary
                                cls
clus                              0  1
  DEL PEAK 11(22Q12.1) MUTATED    5 14
  DEL PEAK 11(22Q12.1) WILD-TYPE  4 84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(22Q12.1) MUTATED      5   14
  DEL PEAK 11(22Q12.1) WILD-TYPE    4   84
                        clus
vv                       DEL PEAK 11(22Q12.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           14
                        clus
vv                       DEL PEAK 11(22Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             84
[1] 2 2
[1] FALSE

Clustering(12) Variable = DEL PEAK 12(22Q13.32) MUTATION ANALYSIS
D12V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 12(22Q13.32) MUTATED   14  0
  DEL PEAK 12(22Q13.32) WILD-TYPE 99  6
  DEL PEAK 12(22Q13.32) MUTATED DEL PEAK 12(22Q13.32) WILD-TYPE 
                             14                             105 
  DEL PEAK 12(22Q13.32) MUTATED DEL PEAK 12(22Q13.32) WILD-TYPE 
                              0                               6 
$`DEL PEAK 12(22Q13.32) MUTATED`
TCGA-3G-AB19 TCGA-3S-A8YW TCGA-4V-A9QJ TCGA-4V-A9QN TCGA-4V-A9QX TCGA-5U-AB0D 
       90.61        13.48        88.83        28.90        11.24        11.57 
TCGA-5U-AB0F TCGA-XM-A8RC TCGA-XU-A92Z TCGA-XU-A936 TCGA-ZB-A963 TCGA-ZB-A969 
       15.09        97.41       120.43        21.14        30.74         0.66 
TCGA-ZB-A96A TCGA-ZB-A96L 
       10.68         0.30 

$`DEL PEAK 12(22Q13.32) WILD-TYPE`
TCGA-3G-AB0O TCGA-3G-AB0Q TCGA-3G-AB0T TCGA-3G-AB14 TCGA-3Q-A9WF TCGA-3S-AAYX 
       56.65        59.15        81.80        17.75        15.35         9.96 
TCGA-3T-AA9L TCGA-4V-A9QI TCGA-4V-A9QL TCGA-4V-A9QM TCGA-4V-A9QQ TCGA-4V-A9QR 
       34.52        89.23        56.75        38.50        45.07        19.76 
TCGA-4V-A9QS TCGA-4V-A9QT TCGA-4V-A9QU TCGA-4V-A9QW TCGA-4X-A9F9 TCGA-4X-A9FA 
       19.76        21.70        16.60        14.07        15.78        12.89 
TCGA-4X-A9FB TCGA-4X-A9FC TCGA-4X-A9FD TCGA-5G-A9ZZ TCGA-5K-AAAP TCGA-5U-AB0E 
       23.57        55.46        39.45        19.50        34.65        10.36 
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        49.22 
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         2.37 
TCGA-X7-A8M0 TCGA-X7-A8M1 TCGA-X7-A8M3 TCGA-X7-A8M4 TCGA-X7-A8M5 TCGA-X7-A8M8 
       14.50        42.15         1.64       125.19        54.08        83.28 
TCGA-XH-A853 TCGA-XM-A8R8 TCGA-XM-A8R9 TCGA-XM-A8RB TCGA-XM-A8RD TCGA-XM-A8RE 
       30.08        52.54        48.92        37.61        50.83         7.69 
TCGA-XM-A8RF TCGA-XM-A8RG TCGA-XM-A8RH TCGA-XM-A8RI TCGA-XM-A8RL TCGA-XM-AAZ1 
       26.20        12.69        11.93        12.72        84.23        13.05 
TCGA-XM-AAZ2 TCGA-XM-AAZ3 TCGA-XU-A92O TCGA-XU-A92Q TCGA-XU-A92R TCGA-XU-A92T 
       32.25        37.81       112.11        35.90        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-A95F 
       50.53        49.38       107.44        18.67        13.32        22.78 
TCGA-YT-A95G TCGA-YT-A95H TCGA-ZB-A961 TCGA-ZB-A962 TCGA-ZB-A964 TCGA-ZB-A965 
       49.78        12.79         0.13         0.20        18.58        16.57 
TCGA-ZB-A966 TCGA-ZB-A96B TCGA-ZB-A96C TCGA-ZB-A96D TCGA-ZB-A96E TCGA-ZB-A96F 
       12.46        60.33        43.43        42.81         0.23         0.16 
TCGA-ZB-A96G TCGA-ZB-A96H TCGA-ZB-A96I TCGA-ZB-A96K TCGA-ZB-A96M TCGA-ZB-A96O 
       32.35        37.48         5.19        31.50         0.46         1.81 
TCGA-ZB-A96P TCGA-ZB-A96Q TCGA-ZB-A96R TCGA-ZB-A96V TCGA-ZC-AAA7 TCGA-ZC-AAAA 
       10.68         7.17        35.34         8.52        28.04        26.93 
TCGA-ZC-AAAF TCGA-ZC-AAAH TCGA-ZL-A9V6 
       38.30        16.34        68.91 

  DEL PEAK 12(22Q13.32) MUTATED DEL PEAK 12(22Q13.32) WILD-TYPE 
                           0.30                            0.13 
  DEL PEAK 12(22Q13.32) MUTATED DEL PEAK 12(22Q13.32) WILD-TYPE 
                         120.43                          149.98 
  DEL PEAK 12(22Q13.32) MUTATED DEL PEAK 12(22Q13.32) WILD-TYPE 
                         18.115                          32.250 
[1] "0.3 - 120.4 (18.1)" "0.1 - 150.0 (32.2)"
[1] "hr="     "8.5e+07"
D12V2, continuous
D12V3, binary
                                 cls
clus                               0  1
  DEL PEAK 12(22Q13.32) MUTATED    9  6
  DEL PEAK 12(22Q13.32) WILD-TYPE 50 56
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 12(22Q13.32) MUTATED      9    6
  DEL PEAK 12(22Q13.32) WILD-TYPE   50   56
        clus
vv       DEL PEAK 12(22Q13.32) MUTATED DEL PEAK 12(22Q13.32) WILD-TYPE
  FEMALE                             9                              50
  MALE                               6                              56
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(22Q13.32) MUTATED       1                         0    14
  DEL PEAK 12(22Q13.32) WILD-TYPE    12                         6    86
D12V4, multiclass
                           clus
vv                          DEL PEAK 12(22Q13.32) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                14
                           clus
vv                          DEL PEAK 12(22Q13.32) WILD-TYPE
  ASIAN                                                  12
  BLACK OR AFRICAN AMERICAN                               6
  WHITE                                                  86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V5, binary
                                 cls
clus                               0  1
  DEL PEAK 12(22Q13.32) MUTATED    4 11
  DEL PEAK 12(22Q13.32) WILD-TYPE  5 87
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 12(22Q13.32) MUTATED      4   11
  DEL PEAK 12(22Q13.32) WILD-TYPE    5   87
                        clus
vv                       DEL PEAK 12(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            11
                        clus
vv                       DEL PEAK 12(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                              87
[1] 2 2
[1] FALSE
