[1] "ofn"       "-oTUVM-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/UVM-TP/15096076/UVM-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UVM-TP/15908354/transformed.cor.cli.txt"

nPatients in clinical file=80, in cluster file=80, common to both=80
[1] "Reduce the number of clustering variables from 22 to 20."
[1] 20 80
[1] "AMP PEAK 1(6P24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(6P24.3) MUTATED AMP PEAK 1(6P24.3) WILD-TYPE 
                          45                           35 
  AMP PEAK 1(6P24.3) MUTATED AMP PEAK 1(6P24.3) WILD-TYPE 
                          45                           35 
[1] "AMP PEAK 2(8Q24.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(8Q24.22) MUTATED AMP PEAK 2(8Q24.22) WILD-TYPE 
                           61                            19 
  AMP PEAK 2(8Q24.22) MUTATED AMP PEAK 2(8Q24.22) WILD-TYPE 
                           61                            19 
[1] "AMP PEAK 3(17Q25.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 3(17Q25.3) MUTATED AMP PEAK 3(17Q25.3) WILD-TYPE 
                           14                            66 
  AMP PEAK 3(17Q25.3) MUTATED AMP PEAK 3(17Q25.3) WILD-TYPE 
                           14                            66 
[1] "DEL PEAK  1(1P36.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            24                             56 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            24                             56 
[1] "DEL PEAK  2(2Q37.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(2Q37.2) MUTATED DEL PEAK  2(2Q37.2) WILD-TYPE 
                            3                            77 
  DEL PEAK  2(2Q37.2) MUTATED DEL PEAK  2(2Q37.2) WILD-TYPE 
                            3                            77 
[1] "DEL PEAK  3(3P25.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(3P25.2) MUTATED DEL PEAK  3(3P25.2) WILD-TYPE 
                           43                            37 
  DEL PEAK  3(3P25.2) MUTATED DEL PEAK  3(3P25.2) WILD-TYPE 
                           43                            37 
[1] "DEL PEAK  4(3P25.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                           43                            37 
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                           43                            37 
[1] "DEL PEAK  5(3P22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P22.2) MUTATED DEL PEAK  5(3P22.2) WILD-TYPE 
                           43                            37 
  DEL PEAK  5(3P22.2) MUTATED DEL PEAK  5(3P22.2) WILD-TYPE 
                           43                            37 
[1] "DEL PEAK  6(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           44                            36 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           44                            36 
[1] "DEL PEAK  7(3Q24) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3Q24) MUTATED DEL PEAK  7(3Q24) WILD-TYPE 
                         44                          36 
  DEL PEAK  7(3Q24) MUTATED DEL PEAK  7(3Q24) WILD-TYPE 
                         44                          36 
[1] "DEL PEAK  8(3Q29) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                         44                          36 
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                         44                          36 
[1] "DEL PEAK  9(5Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(5Q23.1) MUTATED DEL PEAK  9(5Q23.1) WILD-TYPE 
                            4                            76 
  DEL PEAK  9(5Q23.1) MUTATED DEL PEAK  9(5Q23.1) WILD-TYPE 
                            4                            76 
[1] "DEL PEAK 10(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                            24                             56 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                            24                             56 
[1] "DEL PEAK 11(6Q27) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                         24                          56 
  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                         24                          56 
[1] "DEL PEAK 12(8P11.22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(8P11.22) MUTATED DEL PEAK 12(8P11.22) WILD-TYPE 
                            19                             61 
  DEL PEAK 12(8P11.22) MUTATED DEL PEAK 12(8P11.22) WILD-TYPE 
                            19                             61 
[1] "DEL PEAK 15(11Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(11Q24.3) MUTATED DEL PEAK 15(11Q24.3) WILD-TYPE 
                             7                             73 
  DEL PEAK 15(11Q24.3) MUTATED DEL PEAK 15(11Q24.3) WILD-TYPE 
                             7                             73 
[1] "DEL PEAK 16(16Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(16Q12.1) MUTATED DEL PEAK 16(16Q12.1) WILD-TYPE 
                            16                             64 
  DEL PEAK 16(16Q12.1) MUTATED DEL PEAK 16(16Q12.1) WILD-TYPE 
                            16                             64 
[1] "DEL PEAK 17(16Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(16Q23.3) MUTATED DEL PEAK 17(16Q23.3) WILD-TYPE 
                            17                             63 
  DEL PEAK 17(16Q23.3) MUTATED DEL PEAK 17(16Q23.3) WILD-TYPE 
                            17                             63 
[1] "DEL PEAK 18(16Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(16Q24.3) MUTATED DEL PEAK 18(16Q24.3) WILD-TYPE 
                            17                             63 
  DEL PEAK 18(16Q24.3) MUTATED DEL PEAK 18(16Q24.3) WILD-TYPE 
                            17                             63 
[1] "DEL PEAK 19(17Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(17Q12) MUTATED DEL PEAK 19(17Q12) WILD-TYPE 
                           3                           77 
  DEL PEAK 19(17Q12) MUTATED DEL PEAK 19(17Q12) WILD-TYPE 
                           3                           77 
[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] "RADIATIONS_RADIATION_REGIMENINDICATION"
[12] "RACE"                                  
[13] "ETHNICITY"                             
[14] "BATCH_NUMBER"                          

Input Data has 14 rows and 80 columns.

[1] "Batch" "14"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=40,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=13,	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=64,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'NEOPLASM_DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCC_UPLOAD_DATE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE excluded in the analysis because there is no case of (both >= 3) in the table below"
              19-2-2015 2-4-2015
freq.values   "1"       "79"    
freq.contrast "79"      "1"     
both >= 3     "FALSE"   "FALSE" 
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'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 12:'RACE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RACE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "1"                "52"                  
freq.contrast "52"               "1"                   
both >= 3     "FALSE"            "FALSE"               
Variable 14:'BATCH_NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "BATCH_NUMBER excluded in the analysis because there is no case of (both >= 3) in the table below"
              B417.12.0 B417.15.0
freq.values   "1"       "79"     
freq.contrast "79"      "1"      
both >= 3     "FALSE"   "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] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 80 columns, 1 survival variables, and 5 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"        "NEOPLASM_DISEASESTAGE" "PATHOLOGY_T_STAGE"    
[4] "PATHOLOGY_M_STAGE"     "GENDER"               
YEARS_TO_BIRTH, nv=40, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T2 T3 T4 
14 32 34 
[1] "table(vv)"
vv
T2 T3 T4 
14 32 34 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T2 T3 T4 
14 32 34 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T2 T3 T4 
14 32 34 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK 1(6P24.3) MUTATION ANALYSIS
D1V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 1(6P24.3) MUTATED   40  5
  AMP PEAK 1(6P24.3) WILD-TYPE 27  8
  AMP PEAK 1(6P24.3) MUTATED AMP PEAK 1(6P24.3) WILD-TYPE 
                          45                           35 
  AMP PEAK 1(6P24.3) MUTATED AMP PEAK 1(6P24.3) WILD-TYPE 
                           5                            8 
$`AMP PEAK 1(6P24.3) MUTATED`
TCGA-V3-A9ZX TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
        4.50         4.04        74.53        26.56        30.38        24.69 
TCGA-V4-A9EC TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO 
       24.43        13.22        12.56        18.64        22.03        19.53 
TCGA-V4-A9ET TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F2 
       31.66        30.05        24.00        25.02        19.69        12.20 
TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F7 TCGA-VD-A8K7 TCGA-VD-A8K9 TCGA-VD-A8KA 
       22.03        20.22        32.28         0.10         0.46        37.28 
TCGA-VD-A8KB TCGA-VD-A8KE TCGA-VD-A8KG TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KL 
       35.31        26.99         0.66         1.25        31.59        20.98 
TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8S TCGA-WC-A87T TCGA-WC-A87U 
        0.13         2.24        26.14        14.04        70.65        51.98 
TCGA-WC-A87W TCGA-WC-A880 TCGA-WC-A881 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A88A 
       45.57        31.99        22.82         0.39        10.36         2.70 
TCGA-WC-AA9E TCGA-YZ-A982 TCGA-YZ-A983 
       14.20        16.27        17.98 

$`AMP PEAK 1(6P24.3) WILD-TYPE`
TCGA-RZ-AB0B TCGA-V4-A9E7 TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH 
        4.90        13.64        28.41        13.08        27.09        22.03 
TCGA-V4-A9EL TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9F0 
       23.44        14.96        37.81        23.31        27.48        24.10 
TCGA-V4-A9F1 TCGA-V4-A9F5 TCGA-V4-A9F8 TCGA-VD-A8K8 TCGA-VD-A8KD TCGA-VD-A8KF 
       21.73         6.67        19.63        16.87         3.75         1.32 
TCGA-VD-A8KH TCGA-VD-A8KK TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P 
        0.33         2.10         0.20         1.45         7.50         2.83 
TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8T TCGA-WC-A87Y TCGA-WC-A882 TCGA-WC-A883 
        0.23         0.20         0.49        31.40        11.31         7.92 
TCGA-WC-A888 TCGA-WC-AA9A TCGA-YZ-A980 TCGA-YZ-A984 TCGA-YZ-A985 
       10.13        14.89        52.64        42.08        25.81 

  AMP PEAK 1(6P24.3) MUTATED AMP PEAK 1(6P24.3) WILD-TYPE 
                         0.1                          0.2 
  AMP PEAK 1(6P24.3) MUTATED AMP PEAK 1(6P24.3) WILD-TYPE 
                       74.53                        52.64 
  AMP PEAK 1(6P24.3) MUTATED AMP PEAK 1(6P24.3) WILD-TYPE 
                       20.98                        13.64 
[1] "0.1 - 74.5 (21.0)" "0.2 - 52.6 (13.6)"
[1] "hr=" "2.8"
D1V2, continuous
                              vv
clus                           STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  AMP PEAK 1(6P24.3) MUTATED           9        16         14          5
  AMP PEAK 1(6P24.3) WILD-TYPE         3        11         11          5
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 1(6P24.3) MUTATED            0        1
  AMP PEAK 1(6P24.3) WILD-TYPE          1        3
D1V3, multiclass
            clus
vv           AMP PEAK 1(6P24.3) MUTATED AMP PEAK 1(6P24.3) WILD-TYPE
  STAGE IIA                           9                            3
  STAGE IIB                          16                           11
  STAGE IIIA                         14                           11
  STAGE IIIB                          5                            5
  STAGE IIIC                          0                            1
  STAGE IV                            1                            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                           T2 T3 T4
  AMP PEAK 1(6P24.3) MUTATED   10 17 18
  AMP PEAK 1(6P24.3) WILD-TYPE  4 15 16
D1V4, multiclass
    clus
vv   AMP PEAK 1(6P24.3) MUTATED AMP PEAK 1(6P24.3) WILD-TYPE
  T2                         10                            4
  T3                         17                           15
  T4                         18                           16
[1] 3 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
  AMP PEAK 1(6P24.3) MUTATED   27  1
  AMP PEAK 1(6P24.3) WILD-TYPE 24  3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(6P24.3) MUTATED     27    1
  AMP PEAK 1(6P24.3) WILD-TYPE   24    3
   clus
vv  AMP PEAK 1(6P24.3) MUTATED AMP PEAK 1(6P24.3) WILD-TYPE
  0                         27                           24
  1                          1                            3
[1] 2 2
[1] FALSE
D1V6, binary
                              cls
clus                            0  1
  AMP PEAK 1(6P24.3) MUTATED   20 25
  AMP PEAK 1(6P24.3) WILD-TYPE 15 20
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(6P24.3) MUTATED     20   25
  AMP PEAK 1(6P24.3) WILD-TYPE   15   20
        clus
vv       AMP PEAK 1(6P24.3) MUTATED AMP PEAK 1(6P24.3) WILD-TYPE
  FEMALE                         20                           15
  MALE                           25                           20
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK 2(8Q24.22) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 2(8Q24.22) MUTATED   49 12
  AMP PEAK 2(8Q24.22) WILD-TYPE 18  1
  AMP PEAK 2(8Q24.22) MUTATED AMP PEAK 2(8Q24.22) WILD-TYPE 
                           61                            19 
  AMP PEAK 2(8Q24.22) MUTATED AMP PEAK 2(8Q24.22) WILD-TYPE 
                           12                             1 
$`AMP PEAK 2(8Q24.22) MUTATED`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 
        4.90         4.50        74.53        13.64        26.56        30.38 
TCGA-V4-A9EA TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EI TCGA-V4-A9EJ 
       24.69        28.41        13.08        27.09        13.22        12.56 
TCGA-V4-A9EK TCGA-V4-A9EL TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ET 
       18.64        23.44        22.03        19.53        14.96        31.66 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EZ TCGA-V4-A9F0 
       23.31        27.48        30.05        24.00        19.69        24.10 
TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F8 
       21.73        12.20        22.03        20.22         6.67        19.63 
TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KF 
       16.87         0.46        37.28        35.31         3.75         1.32 
TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL 
        0.66         0.33         1.25        31.59         2.10        20.98 
TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8S 
        0.13         2.24         1.45         7.50         2.83        14.04 
TCGA-VD-AA8T TCGA-WC-A87Y TCGA-WC-A881 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A885 
        0.49        31.40        22.82        11.31         7.92        10.36 
TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9A TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A982 
       10.13         2.70        14.89        14.20        52.64        16.27 
TCGA-YZ-A984 
       42.08 

$`AMP PEAK 2(8Q24.22) WILD-TYPE`
TCGA-V3-A9ZY TCGA-V4-A9EC TCGA-V4-A9EH TCGA-V4-A9ES TCGA-V4-A9EY TCGA-V4-A9F7 
        4.04        24.43        22.03        37.81        25.02        32.28 
TCGA-VD-A8K7 TCGA-VD-A8KE TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8Q TCGA-VD-AA8R 
        0.10        26.99        26.14         0.20         0.23         0.20 
TCGA-WC-A87T TCGA-WC-A87U TCGA-WC-A87W TCGA-WC-A880 TCGA-WC-A884 TCGA-YZ-A983 
       70.65        51.98        45.57        31.99         0.39        17.98 
TCGA-YZ-A985 
       25.81 

  AMP PEAK 2(8Q24.22) MUTATED AMP PEAK 2(8Q24.22) WILD-TYPE 
                         0.13                          0.10 
  AMP PEAK 2(8Q24.22) MUTATED AMP PEAK 2(8Q24.22) WILD-TYPE 
                        74.53                         70.65 
  AMP PEAK 2(8Q24.22) MUTATED AMP PEAK 2(8Q24.22) WILD-TYPE 
                        16.27                         25.02 
[1] "0.1 - 74.5 (16.3)" "0.1 - 70.7 (25.0)"
[1] "hr=" "4.9"
D2V2, continuous
                               vv
clus                            STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  AMP PEAK 2(8Q24.22) MUTATED           8        20         19          8
  AMP PEAK 2(8Q24.22) WILD-TYPE         4         7          6          2
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 2(8Q24.22) MUTATED            1        4
  AMP PEAK 2(8Q24.22) WILD-TYPE          0        0
D2V3, multiclass
            clus
vv           AMP PEAK 2(8Q24.22) MUTATED AMP PEAK 2(8Q24.22) WILD-TYPE
  STAGE IIA                            8                             4
  STAGE IIB                           20                             7
  STAGE IIIA                          19                             6
  STAGE IIIB                           8                             2
  STAGE IIIC                           1                             0
  STAGE IV                             4                             0
[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                            T2 T3 T4
  AMP PEAK 2(8Q24.22) MUTATED   10 23 28
  AMP PEAK 2(8Q24.22) WILD-TYPE  4  9  6
D2V4, multiclass
    clus
vv   AMP PEAK 2(8Q24.22) MUTATED AMP PEAK 2(8Q24.22) WILD-TYPE
  T2                          10                             4
  T3                          23                             9
  T4                          28                             6
[1] 3 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
  AMP PEAK 2(8Q24.22) MUTATED   38  4
  AMP PEAK 2(8Q24.22) WILD-TYPE 13  0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 2(8Q24.22) MUTATED     38    4
  AMP PEAK 2(8Q24.22) WILD-TYPE   13    0
   clus
vv  AMP PEAK 2(8Q24.22) MUTATED AMP PEAK 2(8Q24.22) WILD-TYPE
  0                          38                            13
  1                           4                             0
[1] 2 2
[1] FALSE
D2V6, binary
                               cls
clus                             0  1
  AMP PEAK 2(8Q24.22) MUTATED   25 36
  AMP PEAK 2(8Q24.22) WILD-TYPE 10  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 2(8Q24.22) MUTATED     25   36
  AMP PEAK 2(8Q24.22) WILD-TYPE   10    9
        clus
vv       AMP PEAK 2(8Q24.22) MUTATED AMP PEAK 2(8Q24.22) WILD-TYPE
  FEMALE                          25                            10
  MALE                            36                             9
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK 3(17Q25.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 3(17Q25.3) MUTATED   13  1
  AMP PEAK 3(17Q25.3) WILD-TYPE 54 12
  AMP PEAK 3(17Q25.3) MUTATED AMP PEAK 3(17Q25.3) WILD-TYPE 
                           14                            66 
  AMP PEAK 3(17Q25.3) MUTATED AMP PEAK 3(17Q25.3) WILD-TYPE 
                            1                            12 
$`AMP PEAK 3(17Q25.3) MUTATED`
TCGA-V4-A9E8 TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EO TCGA-V4-A9ET TCGA-VD-A8KB 
       26.56        12.56        18.64        19.53        31.66        35.31 
TCGA-VD-A8KL TCGA-VD-AA8M TCGA-VD-AA8O TCGA-VD-AA8S TCGA-WC-A884 TCGA-WC-A885 
       20.98         0.20         7.50        14.04         0.39        10.36 
TCGA-YZ-A982 TCGA-YZ-A984 
       16.27        42.08 

$`AMP PEAK 3(17Q25.3) WILD-TYPE`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E9 
        4.90         4.50         4.04        74.53        13.64        30.38 
TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH 
       24.69        24.43        28.41        13.08        27.09        22.03 
TCGA-V4-A9EI TCGA-V4-A9EL TCGA-V4-A9EM TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9EU 
       13.22        23.44        22.03        14.96        37.81        23.31 
TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 
       27.48        30.05        24.00        25.02        19.69        24.10 
TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 
       21.73        12.20        22.03        20.22         6.67        32.28 
TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KD 
       19.63         0.10        16.87         0.46        37.28         3.75 
TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ 
       26.99         1.32         0.66         0.33         1.25        31.59 
TCGA-VD-A8KK TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8N TCGA-VD-AA8P 
        2.10         0.13         2.24        26.14         1.45         2.83 
TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87U TCGA-WC-A87W 
        0.23         0.20         0.49        70.65        51.98        45.57 
TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A881 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A888 
       31.40        31.99        22.82        11.31         7.92        10.13 
TCGA-WC-A88A TCGA-WC-AA9A TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A983 TCGA-YZ-A985 
        2.70        14.89        14.20        52.64        17.98        25.81 

  AMP PEAK 3(17Q25.3) MUTATED AMP PEAK 3(17Q25.3) WILD-TYPE 
                          0.2                           0.1 
  AMP PEAK 3(17Q25.3) MUTATED AMP PEAK 3(17Q25.3) WILD-TYPE 
                        42.08                         74.53 
  AMP PEAK 3(17Q25.3) MUTATED AMP PEAK 3(17Q25.3) WILD-TYPE 
                       17.455                        19.660 
[1] "0.2 - 42.1 (17.5)" "0.1 - 74.5 (19.7)"
[1] "hr=" "2.4"
D3V2, continuous
                               vv
clus                            STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  AMP PEAK 3(17Q25.3) MUTATED           3         6          2          3
  AMP PEAK 3(17Q25.3) WILD-TYPE         9        21         23          7
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 3(17Q25.3) MUTATED            0        0
  AMP PEAK 3(17Q25.3) WILD-TYPE          1        4
D3V3, multiclass
            clus
vv           AMP PEAK 3(17Q25.3) MUTATED AMP PEAK 3(17Q25.3) WILD-TYPE
  STAGE IIA                            3                             9
  STAGE IIB                            6                            21
  STAGE IIIA                           2                            23
  STAGE IIIB                           3                             7
  STAGE IIIC                           0                             1
  STAGE IV                             0                             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                            T2 T3 T4
  AMP PEAK 3(17Q25.3) MUTATED    3  6  5
  AMP PEAK 3(17Q25.3) WILD-TYPE 11 26 29
D3V4, multiclass
    clus
vv   AMP PEAK 3(17Q25.3) MUTATED AMP PEAK 3(17Q25.3) WILD-TYPE
  T2                           3                            11
  T3                           6                            26
  T4                           5                            29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
                               cls
clus                             0  1
  AMP PEAK 3(17Q25.3) MUTATED   10  0
  AMP PEAK 3(17Q25.3) WILD-TYPE 41  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(17Q25.3) MUTATED     10    0
  AMP PEAK 3(17Q25.3) WILD-TYPE   41    4
   clus
vv  AMP PEAK 3(17Q25.3) MUTATED AMP PEAK 3(17Q25.3) WILD-TYPE
  0                          10                            41
  1                           0                             4
[1] 2 2
[1] FALSE
D3V6, binary
                               cls
clus                             0  1
  AMP PEAK 3(17Q25.3) MUTATED    6  8
  AMP PEAK 3(17Q25.3) WILD-TYPE 29 37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(17Q25.3) MUTATED      6    8
  AMP PEAK 3(17Q25.3) WILD-TYPE   29   37
        clus
vv       AMP PEAK 3(17Q25.3) MUTATED AMP PEAK 3(17Q25.3) WILD-TYPE
  FEMALE                           6                            29
  MALE                             8                            37
[1] 2 2
[1] FALSE

Clustering(4) Variable = DEL PEAK  1(1P36.21) MUTATION ANALYSIS
D4V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.21) MUTATED   17  7
  DEL PEAK  1(1P36.21) WILD-TYPE 50  6
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            24                             56 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                             7                              6 
$`DEL PEAK  1(1P36.21) MUTATED`
TCGA-RZ-AB0B TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9EE TCGA-V4-A9EO TCGA-V4-A9EQ 
        4.90        13.64        26.56        13.08        19.53        14.96 
TCGA-V4-A9ES TCGA-V4-A9EW TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F5 TCGA-V4-A9F8 
       37.81        30.05        19.69        24.10         6.67        19.63 
TCGA-VD-A8KA TCGA-VD-A8KH TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8T TCGA-WC-A87W 
       37.28         0.33         7.50         2.83         0.49        45.57 
TCGA-WC-A881 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-AA9A TCGA-WC-AA9E TCGA-YZ-A982 
       22.82        11.31         7.92        14.89        14.20        16.27 

$`DEL PEAK  1(1P36.21) WILD-TYPE`
TCGA-V3-A9ZX TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC 
        4.50         4.04        74.53        30.38        24.69        24.43 
TCGA-V4-A9ED TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EK 
       28.41        27.09        22.03        13.22        12.56        18.64 
TCGA-V4-A9EL TCGA-V4-A9EM TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EX 
       23.44        22.03        31.66        23.31        27.48        24.00 
TCGA-V4-A9EY TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F7 
       25.02        21.73        12.20        22.03        20.22        32.28 
TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE 
        0.10        16.87         0.46        35.31         3.75        26.99 
TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL 
        1.32         0.66         1.25        31.59         2.10        20.98 
TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8Q 
        0.13         2.24        26.14         0.20         1.45         0.23 
TCGA-VD-AA8R TCGA-VD-AA8S TCGA-WC-A87T TCGA-WC-A87U TCGA-WC-A87Y TCGA-WC-A880 
        0.20        14.04        70.65        51.98        31.40        31.99 
TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-YZ-A980 TCGA-YZ-A983 
        0.39        10.36        10.13         2.70        52.64        17.98 
TCGA-YZ-A984 TCGA-YZ-A985 
       42.08        25.81 

  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                          0.33                           0.10 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                         45.57                          74.53 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                        14.925                         21.355 
[1] "0.3 - 45.6 (14.9)" "0.1 - 74.5 (21.4)"
[1] "hr=" "3.3"
D4V2, continuous
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.21) MUTATED           4         7          8          3
  DEL PEAK  1(1P36.21) WILD-TYPE         8        20         17          7
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK  1(1P36.21) MUTATED            0        2
  DEL PEAK  1(1P36.21) WILD-TYPE          1        2
D4V3, multiclass
            clus
vv           DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  STAGE IIA                             4                              8
  STAGE IIB                             7                             20
  STAGE IIIA                            8                             17
  STAGE IIIB                            3                              7
  STAGE IIIC                            0                              1
  STAGE IV                              2                              2
[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                             T2 T3 T4
  DEL PEAK  1(1P36.21) MUTATED    5  8 11
  DEL PEAK  1(1P36.21) WILD-TYPE  9 24 23
D4V4, multiclass
    clus
vv   DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  T2                            5                              9
  T3                            8                             24
  T4                           11                             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.21) MUTATED   17  2
  DEL PEAK  1(1P36.21) WILD-TYPE 34  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED     17    2
  DEL PEAK  1(1P36.21) WILD-TYPE   34    2
   clus
vv  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  0                           17                             34
  1                            2                              2
[1] 2 2
[1] FALSE
D4V6, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.21) MUTATED   12 12
  DEL PEAK  1(1P36.21) WILD-TYPE 23 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED     12   12
  DEL PEAK  1(1P36.21) WILD-TYPE   23   33
        clus
vv       DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  FEMALE                           12                             23
  MALE                             12                             33
[1] 2 2
[1] FALSE

Clustering(5) Variable = DEL PEAK  2(2Q37.2) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(2Q37.2) MUTATED    3  0
  DEL PEAK  2(2Q37.2) WILD-TYPE 64 13
  DEL PEAK  2(2Q37.2) MUTATED DEL PEAK  2(2Q37.2) WILD-TYPE 
                            3                            77 
  DEL PEAK  2(2Q37.2) MUTATED DEL PEAK  2(2Q37.2) WILD-TYPE 
                            0                            13 
$`DEL PEAK  2(2Q37.2) MUTATED`
TCGA-V4-A9EK TCGA-VD-A8K9 TCGA-WC-A87T 
       18.64         0.46        70.65 

$`DEL PEAK  2(2Q37.2) WILD-TYPE`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 
        4.90         4.50         4.04        74.53        13.64        26.56 
TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF 
       30.38        24.69        24.43        28.41        13.08        27.09 
TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EL TCGA-V4-A9EM TCGA-V4-A9EO 
       22.03        13.22        12.56        23.44        22.03        19.53 
TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW 
       14.96        37.81        31.66        23.31        27.48        30.05 
TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 
       24.00        25.02        19.69        24.10        21.73        12.20 
TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 
       22.03        20.22         6.67        32.28        19.63         0.10 
TCGA-VD-A8K8 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF 
       16.87        37.28        35.31         3.75        26.99         1.32 
TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL 
        0.66         0.33         1.25        31.59         2.10        20.98 
TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O 
        0.13         2.24        26.14         0.20         1.45         7.50 
TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87U 
        2.83         0.23         0.20        14.04         0.49        51.98 
TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A881 TCGA-WC-A882 TCGA-WC-A883 
       45.57        31.40        31.99        22.82        11.31         7.92 
TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9A TCGA-WC-AA9E 
        0.39        10.36        10.13         2.70        14.89        14.20 
TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       52.64        16.27        17.98        42.08        25.81 

  DEL PEAK  2(2Q37.2) MUTATED DEL PEAK  2(2Q37.2) WILD-TYPE 
                         0.46                          0.10 
  DEL PEAK  2(2Q37.2) MUTATED DEL PEAK  2(2Q37.2) WILD-TYPE 
                        70.65                         74.53 
  DEL PEAK  2(2Q37.2) MUTATED DEL PEAK  2(2Q37.2) WILD-TYPE 
                        18.64                         19.53 
[1] "0.5 - 70.7 (18.6)" "0.1 - 74.5 (19.5)"
[1] "hr="   "3e+07"
D5V2, continuous
                               vv
clus                            STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  DEL PEAK  2(2Q37.2) MUTATED           1         2          0          0
  DEL PEAK  2(2Q37.2) WILD-TYPE        11        25         25         10
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  2(2Q37.2) MUTATED            0        0
  DEL PEAK  2(2Q37.2) WILD-TYPE          1        4
D5V3, multiclass
            clus
vv           DEL PEAK  2(2Q37.2) MUTATED DEL PEAK  2(2Q37.2) WILD-TYPE
  STAGE IIA                            1                            11
  STAGE IIB                            2                            25
  STAGE IIIA                           0                            25
  STAGE IIIB                           0                            10
  STAGE IIIC                           0                             1
  STAGE IV                             0                             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                            T2 T3 T4
  DEL PEAK  2(2Q37.2) MUTATED    1  2  0
  DEL PEAK  2(2Q37.2) WILD-TYPE 13 30 34
D5V4, multiclass
    clus
vv   DEL PEAK  2(2Q37.2) MUTATED DEL PEAK  2(2Q37.2) WILD-TYPE
  T2                           1                            13
  T3                           2                            30
  T4                           0                            34
[1] 3 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  2(2Q37.2) MUTATED    2  0
  DEL PEAK  2(2Q37.2) WILD-TYPE 49  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2Q37.2) MUTATED      2    0
  DEL PEAK  2(2Q37.2) WILD-TYPE   49    4
   clus
vv  DEL PEAK  2(2Q37.2) MUTATED DEL PEAK  2(2Q37.2) WILD-TYPE
  0                           2                            49
  1                           0                             4
[1] 2 2
[1] FALSE
D5V6, binary
                               cls
clus                             0  1
  DEL PEAK  2(2Q37.2) MUTATED    2  1
  DEL PEAK  2(2Q37.2) WILD-TYPE 33 44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2Q37.2) MUTATED      2    1
  DEL PEAK  2(2Q37.2) WILD-TYPE   33   44
        clus
vv       DEL PEAK  2(2Q37.2) MUTATED DEL PEAK  2(2Q37.2) WILD-TYPE
  FEMALE                           2                            33
  MALE                             1                            44
[1] 2 2
[1] FALSE

Clustering(6) Variable = DEL PEAK  3(3P25.2) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  3(3P25.2) MUTATED   31 12
  DEL PEAK  3(3P25.2) WILD-TYPE 36  1
  DEL PEAK  3(3P25.2) MUTATED DEL PEAK  3(3P25.2) WILD-TYPE 
                           43                            37 
  DEL PEAK  3(3P25.2) MUTATED DEL PEAK  3(3P25.2) WILD-TYPE 
                           12                             1 
$`DEL PEAK  3(3P25.2) MUTATED`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9ED TCGA-V4-A9EE 
        4.90         4.50        13.64        26.56        28.41        13.08 
TCGA-V4-A9EF TCGA-V4-A9EI TCGA-V4-A9EL TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES 
       27.09        13.22        23.44        19.53        14.96        37.81 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9F0 TCGA-V4-A9F1 
       23.31        27.48        30.05        24.00        24.10        21.73 
TCGA-V4-A9F3 TCGA-V4-A9F5 TCGA-V4-A9F8 TCGA-VD-A8K8 TCGA-VD-A8KA TCGA-VD-A8KD 
       22.03         6.67        19.63        16.87        37.28         3.75 
TCGA-VD-A8KF TCGA-VD-A8KI TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN 
        1.32         1.25         2.10        20.98         0.13         2.24 
TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8T TCGA-WC-A87Y TCGA-WC-A882 
        1.45         7.50         2.83         0.49        31.40        11.31 
TCGA-WC-A883 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9A TCGA-YZ-A980 TCGA-YZ-A984 
        7.92        10.13         2.70        14.89        52.64        42.08 
TCGA-YZ-A985 
       25.81 

$`DEL PEAK  3(3P25.2) WILD-TYPE`
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9EH 
        4.04        74.53        30.38        24.69        24.43        22.03 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9ET TCGA-V4-A9EY TCGA-V4-A9EZ 
       12.56        18.64        22.03        31.66        25.02        19.69 
TCGA-V4-A9F2 TCGA-V4-A9F4 TCGA-V4-A9F7 TCGA-VD-A8K7 TCGA-VD-A8K9 TCGA-VD-A8KB 
       12.20        20.22        32.28         0.10         0.46        35.31 
TCGA-VD-A8KE TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KJ TCGA-VD-A8KO TCGA-VD-AA8M 
       26.99         0.66         0.33        31.59        26.14         0.20 
TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-WC-A87T TCGA-WC-A87U TCGA-WC-A87W 
        0.23         0.20        14.04        70.65        51.98        45.57 
TCGA-WC-A880 TCGA-WC-A881 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-AA9E TCGA-YZ-A982 
       31.99        22.82         0.39        10.36        14.20        16.27 
TCGA-YZ-A983 
       17.98 

  DEL PEAK  3(3P25.2) MUTATED DEL PEAK  3(3P25.2) WILD-TYPE 
                         0.13                          0.10 
  DEL PEAK  3(3P25.2) MUTATED DEL PEAK  3(3P25.2) WILD-TYPE 
                        52.64                         74.53 
  DEL PEAK  3(3P25.2) MUTATED DEL PEAK  3(3P25.2) WILD-TYPE 
                        14.96                         20.22 
[1] "0.1 - 52.6 (15.0)" "0.1 - 74.5 (20.2)"
[1] "hr=" "13" 
D6V2, continuous
                               vv
clus                            STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  DEL PEAK  3(3P25.2) MUTATED           3        14         16          4
  DEL PEAK  3(3P25.2) WILD-TYPE         9        13          9          6
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  3(3P25.2) MUTATED            1        4
  DEL PEAK  3(3P25.2) WILD-TYPE          0        0
D6V3, multiclass
            clus
vv           DEL PEAK  3(3P25.2) MUTATED DEL PEAK  3(3P25.2) WILD-TYPE
  STAGE IIA                            3                             9
  STAGE IIB                           14                            13
  STAGE IIIA                          16                             9
  STAGE IIIB                           4                             6
  STAGE IIIC                           1                             0
  STAGE IV                             4                             0
[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                            T2 T3 T4
  DEL PEAK  3(3P25.2) MUTATED    5 17 21
  DEL PEAK  3(3P25.2) WILD-TYPE  9 15 13
D6V4, multiclass
    clus
vv   DEL PEAK  3(3P25.2) MUTATED DEL PEAK  3(3P25.2) WILD-TYPE
  T2                           5                             9
  T3                          17                            15
  T4                          21                            13
[1] 3 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  3(3P25.2) MUTATED   26  4
  DEL PEAK  3(3P25.2) WILD-TYPE 25  0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(3P25.2) MUTATED     26    4
  DEL PEAK  3(3P25.2) WILD-TYPE   25    0
   clus
vv  DEL PEAK  3(3P25.2) MUTATED DEL PEAK  3(3P25.2) WILD-TYPE
  0                          26                            25
  1                           4                             0
[1] 2 2
[1] FALSE
D6V6, binary
                               cls
clus                             0  1
  DEL PEAK  3(3P25.2) MUTATED   19 24
  DEL PEAK  3(3P25.2) WILD-TYPE 16 21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(3P25.2) MUTATED     19   24
  DEL PEAK  3(3P25.2) WILD-TYPE   16   21
        clus
vv       DEL PEAK  3(3P25.2) MUTATED DEL PEAK  3(3P25.2) WILD-TYPE
  FEMALE                          19                            16
  MALE                            24                            21
[1] 2 2
[1] FALSE

Clustering(7) Variable = DEL PEAK  4(3P25.1) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(3P25.1) MUTATED   31 12
  DEL PEAK  4(3P25.1) WILD-TYPE 36  1
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                           43                            37 
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                           12                             1 
$`DEL PEAK  4(3P25.1) MUTATED`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9ED TCGA-V4-A9EE 
        4.90         4.50        13.64        26.56        28.41        13.08 
TCGA-V4-A9EF TCGA-V4-A9EI TCGA-V4-A9EL TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES 
       27.09        13.22        23.44        19.53        14.96        37.81 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9F0 TCGA-V4-A9F1 
       23.31        27.48        30.05        24.00        24.10        21.73 
TCGA-V4-A9F3 TCGA-V4-A9F5 TCGA-V4-A9F8 TCGA-VD-A8K8 TCGA-VD-A8KA TCGA-VD-A8KD 
       22.03         6.67        19.63        16.87        37.28         3.75 
TCGA-VD-A8KF TCGA-VD-A8KI TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN 
        1.32         1.25         2.10        20.98         0.13         2.24 
TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8T TCGA-WC-A87Y TCGA-WC-A882 
        1.45         7.50         2.83         0.49        31.40        11.31 
TCGA-WC-A883 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9A TCGA-YZ-A980 TCGA-YZ-A984 
        7.92        10.13         2.70        14.89        52.64        42.08 
TCGA-YZ-A985 
       25.81 

$`DEL PEAK  4(3P25.1) WILD-TYPE`
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9EH 
        4.04        74.53        30.38        24.69        24.43        22.03 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9ET TCGA-V4-A9EY TCGA-V4-A9EZ 
       12.56        18.64        22.03        31.66        25.02        19.69 
TCGA-V4-A9F2 TCGA-V4-A9F4 TCGA-V4-A9F7 TCGA-VD-A8K7 TCGA-VD-A8K9 TCGA-VD-A8KB 
       12.20        20.22        32.28         0.10         0.46        35.31 
TCGA-VD-A8KE TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KJ TCGA-VD-A8KO TCGA-VD-AA8M 
       26.99         0.66         0.33        31.59        26.14         0.20 
TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-WC-A87T TCGA-WC-A87U TCGA-WC-A87W 
        0.23         0.20        14.04        70.65        51.98        45.57 
TCGA-WC-A880 TCGA-WC-A881 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-AA9E TCGA-YZ-A982 
       31.99        22.82         0.39        10.36        14.20        16.27 
TCGA-YZ-A983 
       17.98 

  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                         0.13                          0.10 
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                        52.64                         74.53 
  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE 
                        14.96                         20.22 
[1] "0.1 - 52.6 (15.0)" "0.1 - 74.5 (20.2)"
[1] "hr=" "13" 
D7V2, continuous
                               vv
clus                            STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  DEL PEAK  4(3P25.1) MUTATED           3        14         16          4
  DEL PEAK  4(3P25.1) WILD-TYPE         9        13          9          6
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  4(3P25.1) MUTATED            1        4
  DEL PEAK  4(3P25.1) WILD-TYPE          0        0
D7V3, multiclass
            clus
vv           DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE
  STAGE IIA                            3                             9
  STAGE IIB                           14                            13
  STAGE IIIA                          16                             9
  STAGE IIIB                           4                             6
  STAGE IIIC                           1                             0
  STAGE IV                             4                             0
[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                            T2 T3 T4
  DEL PEAK  4(3P25.1) MUTATED    5 17 21
  DEL PEAK  4(3P25.1) WILD-TYPE  9 15 13
D7V4, multiclass
    clus
vv   DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE
  T2                           5                             9
  T3                          17                            15
  T4                          21                            13
[1] 3 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  4(3P25.1) MUTATED   26  4
  DEL PEAK  4(3P25.1) WILD-TYPE 25  0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P25.1) MUTATED     26    4
  DEL PEAK  4(3P25.1) WILD-TYPE   25    0
   clus
vv  DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE
  0                          26                            25
  1                           4                             0
[1] 2 2
[1] FALSE
D7V6, binary
                               cls
clus                             0  1
  DEL PEAK  4(3P25.1) MUTATED   19 24
  DEL PEAK  4(3P25.1) WILD-TYPE 16 21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P25.1) MUTATED     19   24
  DEL PEAK  4(3P25.1) WILD-TYPE   16   21
        clus
vv       DEL PEAK  4(3P25.1) MUTATED DEL PEAK  4(3P25.1) WILD-TYPE
  FEMALE                          19                            16
  MALE                            24                            21
[1] 2 2
[1] FALSE

Clustering(8) Variable = DEL PEAK  5(3P22.2) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(3P22.2) MUTATED   31 12
  DEL PEAK  5(3P22.2) WILD-TYPE 36  1
  DEL PEAK  5(3P22.2) MUTATED DEL PEAK  5(3P22.2) WILD-TYPE 
                           43                            37 
  DEL PEAK  5(3P22.2) MUTATED DEL PEAK  5(3P22.2) WILD-TYPE 
                           12                             1 
$`DEL PEAK  5(3P22.2) MUTATED`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9ED TCGA-V4-A9EE 
        4.90         4.50        13.64        26.56        28.41        13.08 
TCGA-V4-A9EF TCGA-V4-A9EI TCGA-V4-A9EL TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES 
       27.09        13.22        23.44        19.53        14.96        37.81 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9F0 TCGA-V4-A9F1 
       23.31        27.48        30.05        24.00        24.10        21.73 
TCGA-V4-A9F3 TCGA-V4-A9F5 TCGA-V4-A9F8 TCGA-VD-A8K8 TCGA-VD-A8KA TCGA-VD-A8KD 
       22.03         6.67        19.63        16.87        37.28         3.75 
TCGA-VD-A8KF TCGA-VD-A8KI TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN 
        1.32         1.25         2.10        20.98         0.13         2.24 
TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8T TCGA-WC-A87Y TCGA-WC-A882 
        1.45         7.50         2.83         0.49        31.40        11.31 
TCGA-WC-A883 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9A TCGA-YZ-A980 TCGA-YZ-A984 
        7.92        10.13         2.70        14.89        52.64        42.08 
TCGA-YZ-A985 
       25.81 

$`DEL PEAK  5(3P22.2) WILD-TYPE`
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9EH 
        4.04        74.53        30.38        24.69        24.43        22.03 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9ET TCGA-V4-A9EY TCGA-V4-A9EZ 
       12.56        18.64        22.03        31.66        25.02        19.69 
TCGA-V4-A9F2 TCGA-V4-A9F4 TCGA-V4-A9F7 TCGA-VD-A8K7 TCGA-VD-A8K9 TCGA-VD-A8KB 
       12.20        20.22        32.28         0.10         0.46        35.31 
TCGA-VD-A8KE TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KJ TCGA-VD-A8KO TCGA-VD-AA8M 
       26.99         0.66         0.33        31.59        26.14         0.20 
TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-WC-A87T TCGA-WC-A87U TCGA-WC-A87W 
        0.23         0.20        14.04        70.65        51.98        45.57 
TCGA-WC-A880 TCGA-WC-A881 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-AA9E TCGA-YZ-A982 
       31.99        22.82         0.39        10.36        14.20        16.27 
TCGA-YZ-A983 
       17.98 

  DEL PEAK  5(3P22.2) MUTATED DEL PEAK  5(3P22.2) WILD-TYPE 
                         0.13                          0.10 
  DEL PEAK  5(3P22.2) MUTATED DEL PEAK  5(3P22.2) WILD-TYPE 
                        52.64                         74.53 
  DEL PEAK  5(3P22.2) MUTATED DEL PEAK  5(3P22.2) WILD-TYPE 
                        14.96                         20.22 
[1] "0.1 - 52.6 (15.0)" "0.1 - 74.5 (20.2)"
[1] "hr=" "13" 
D8V2, continuous
                               vv
clus                            STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  DEL PEAK  5(3P22.2) MUTATED           3        14         16          4
  DEL PEAK  5(3P22.2) WILD-TYPE         9        13          9          6
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  5(3P22.2) MUTATED            1        4
  DEL PEAK  5(3P22.2) WILD-TYPE          0        0
D8V3, multiclass
            clus
vv           DEL PEAK  5(3P22.2) MUTATED DEL PEAK  5(3P22.2) WILD-TYPE
  STAGE IIA                            3                             9
  STAGE IIB                           14                            13
  STAGE IIIA                          16                             9
  STAGE IIIB                           4                             6
  STAGE IIIC                           1                             0
  STAGE IV                             4                             0
[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                            T2 T3 T4
  DEL PEAK  5(3P22.2) MUTATED    5 17 21
  DEL PEAK  5(3P22.2) WILD-TYPE  9 15 13
D8V4, multiclass
    clus
vv   DEL PEAK  5(3P22.2) MUTATED DEL PEAK  5(3P22.2) WILD-TYPE
  T2                           5                             9
  T3                          17                            15
  T4                          21                            13
[1] 3 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  5(3P22.2) MUTATED   26  4
  DEL PEAK  5(3P22.2) WILD-TYPE 25  0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P22.2) MUTATED     26    4
  DEL PEAK  5(3P22.2) WILD-TYPE   25    0
   clus
vv  DEL PEAK  5(3P22.2) MUTATED DEL PEAK  5(3P22.2) WILD-TYPE
  0                          26                            25
  1                           4                             0
[1] 2 2
[1] FALSE
D8V6, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P22.2) MUTATED   19 24
  DEL PEAK  5(3P22.2) WILD-TYPE 16 21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P22.2) MUTATED     19   24
  DEL PEAK  5(3P22.2) WILD-TYPE   16   21
        clus
vv       DEL PEAK  5(3P22.2) MUTATED DEL PEAK  5(3P22.2) WILD-TYPE
  FEMALE                          19                            16
  MALE                            24                            21
[1] 2 2
[1] FALSE

Clustering(9) Variable = DEL PEAK  6(3P14.2) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(3P14.2) MUTATED   32 12
  DEL PEAK  6(3P14.2) WILD-TYPE 35  1
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           44                            36 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           12                             1 
$`DEL PEAK  6(3P14.2) MUTATED`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9ED TCGA-V4-A9EE 
        4.90         4.50        13.64        26.56        28.41        13.08 
TCGA-V4-A9EF TCGA-V4-A9EI TCGA-V4-A9EL TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES 
       27.09        13.22        23.44        19.53        14.96        37.81 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9F0 TCGA-V4-A9F1 
       23.31        27.48        30.05        24.00        24.10        21.73 
TCGA-V4-A9F3 TCGA-V4-A9F5 TCGA-V4-A9F8 TCGA-VD-A8K8 TCGA-VD-A8KA TCGA-VD-A8KD 
       22.03         6.67        19.63        16.87        37.28         3.75 
TCGA-VD-A8KF TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM 
        1.32         0.33         1.25         2.10        20.98         0.13 
TCGA-VD-A8KN TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8T TCGA-WC-A87Y 
        2.24         1.45         7.50         2.83         0.49        31.40 
TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9A TCGA-YZ-A980 
       11.31         7.92        10.13         2.70        14.89        52.64 
TCGA-YZ-A984 TCGA-YZ-A985 
       42.08        25.81 

$`DEL PEAK  6(3P14.2) WILD-TYPE`
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9EH 
        4.04        74.53        30.38        24.69        24.43        22.03 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9ET TCGA-V4-A9EY TCGA-V4-A9EZ 
       12.56        18.64        22.03        31.66        25.02        19.69 
TCGA-V4-A9F2 TCGA-V4-A9F4 TCGA-V4-A9F7 TCGA-VD-A8K7 TCGA-VD-A8K9 TCGA-VD-A8KB 
       12.20        20.22        32.28         0.10         0.46        35.31 
TCGA-VD-A8KE TCGA-VD-A8KG TCGA-VD-A8KJ TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8Q 
       26.99         0.66        31.59        26.14         0.20         0.23 
TCGA-VD-AA8R TCGA-VD-AA8S TCGA-WC-A87T TCGA-WC-A87U TCGA-WC-A87W TCGA-WC-A880 
        0.20        14.04        70.65        51.98        45.57        31.99 
TCGA-WC-A881 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-AA9E TCGA-YZ-A982 TCGA-YZ-A983 
       22.82         0.39        10.36        14.20        16.27        17.98 

  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                         0.13                          0.10 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                        52.64                         74.53 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                       14.925                        21.125 
[1] "0.1 - 52.6 (14.9)" "0.1 - 74.5 (21.1)"
[1] "hr=" "13" 
D9V2, continuous
                               vv
clus                            STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  DEL PEAK  6(3P14.2) MUTATED           3        14         16          5
  DEL PEAK  6(3P14.2) WILD-TYPE         9        13          9          5
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  6(3P14.2) MUTATED            1        4
  DEL PEAK  6(3P14.2) WILD-TYPE          0        0
D9V3, multiclass
            clus
vv           DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  STAGE IIA                            3                             9
  STAGE IIB                           14                            13
  STAGE IIIA                          16                             9
  STAGE IIIB                           5                             5
  STAGE IIIC                           1                             0
  STAGE IV                             4                             0
[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                            T2 T3 T4
  DEL PEAK  6(3P14.2) MUTATED    5 17 22
  DEL PEAK  6(3P14.2) WILD-TYPE  9 15 12
D9V4, multiclass
    clus
vv   DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  T2                           5                             9
  T3                          17                            15
  T4                          22                            12
[1] 3 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  6(3P14.2) MUTATED   26  4
  DEL PEAK  6(3P14.2) WILD-TYPE 25  0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     26    4
  DEL PEAK  6(3P14.2) WILD-TYPE   25    0
   clus
vv  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  0                          26                            25
  1                           4                             0
[1] 2 2
[1] FALSE
D9V6, binary
                               cls
clus                             0  1
  DEL PEAK  6(3P14.2) MUTATED   19 25
  DEL PEAK  6(3P14.2) WILD-TYPE 16 20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     19   25
  DEL PEAK  6(3P14.2) WILD-TYPE   16   20
        clus
vv       DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  FEMALE                          19                            16
  MALE                            25                            20
[1] 2 2
[1] FALSE

Clustering(10) Variable = DEL PEAK  7(3Q24) MUTATION ANALYSIS
D10V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  7(3Q24) MUTATED   32 12
  DEL PEAK  7(3Q24) WILD-TYPE 35  1
  DEL PEAK  7(3Q24) MUTATED DEL PEAK  7(3Q24) WILD-TYPE 
                         44                          36 
  DEL PEAK  7(3Q24) MUTATED DEL PEAK  7(3Q24) WILD-TYPE 
                         12                           1 
$`DEL PEAK  7(3Q24) MUTATED`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9ED TCGA-V4-A9EE 
        4.90         4.50        13.64        26.56        28.41        13.08 
TCGA-V4-A9EF TCGA-V4-A9EI TCGA-V4-A9EL TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES 
       27.09        13.22        23.44        19.53        14.96        37.81 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9F0 TCGA-V4-A9F1 
       23.31        27.48        30.05        24.00        24.10        21.73 
TCGA-V4-A9F3 TCGA-V4-A9F5 TCGA-V4-A9F8 TCGA-VD-A8K8 TCGA-VD-A8KA TCGA-VD-A8KD 
       22.03         6.67        19.63        16.87        37.28         3.75 
TCGA-VD-A8KF TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM 
        1.32         0.33         1.25         2.10        20.98         0.13 
TCGA-VD-A8KN TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8T TCGA-WC-A87Y 
        2.24         1.45         7.50         2.83         0.49        31.40 
TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9A TCGA-YZ-A980 
       11.31         7.92        10.13         2.70        14.89        52.64 
TCGA-YZ-A984 TCGA-YZ-A985 
       42.08        25.81 

$`DEL PEAK  7(3Q24) WILD-TYPE`
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9EH 
        4.04        74.53        30.38        24.69        24.43        22.03 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9ET TCGA-V4-A9EY TCGA-V4-A9EZ 
       12.56        18.64        22.03        31.66        25.02        19.69 
TCGA-V4-A9F2 TCGA-V4-A9F4 TCGA-V4-A9F7 TCGA-VD-A8K7 TCGA-VD-A8K9 TCGA-VD-A8KB 
       12.20        20.22        32.28         0.10         0.46        35.31 
TCGA-VD-A8KE TCGA-VD-A8KG TCGA-VD-A8KJ TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8Q 
       26.99         0.66        31.59        26.14         0.20         0.23 
TCGA-VD-AA8R TCGA-VD-AA8S TCGA-WC-A87T TCGA-WC-A87U TCGA-WC-A87W TCGA-WC-A880 
        0.20        14.04        70.65        51.98        45.57        31.99 
TCGA-WC-A881 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-AA9E TCGA-YZ-A982 TCGA-YZ-A983 
       22.82         0.39        10.36        14.20        16.27        17.98 

  DEL PEAK  7(3Q24) MUTATED DEL PEAK  7(3Q24) WILD-TYPE 
                       0.13                        0.10 
  DEL PEAK  7(3Q24) MUTATED DEL PEAK  7(3Q24) WILD-TYPE 
                      52.64                       74.53 
  DEL PEAK  7(3Q24) MUTATED DEL PEAK  7(3Q24) WILD-TYPE 
                     14.925                      21.125 
[1] "0.1 - 52.6 (14.9)" "0.1 - 74.5 (21.1)"
[1] "hr=" "13" 
D10V2, continuous
                             vv
clus                          STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  DEL PEAK  7(3Q24) MUTATED           3        14         16          5
  DEL PEAK  7(3Q24) WILD-TYPE         9        13          9          5
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK  7(3Q24) MUTATED            1        4
  DEL PEAK  7(3Q24) WILD-TYPE          0        0
D10V3, multiclass
            clus
vv           DEL PEAK  7(3Q24) MUTATED DEL PEAK  7(3Q24) WILD-TYPE
  STAGE IIA                          3                           9
  STAGE IIB                         14                          13
  STAGE IIIA                        16                           9
  STAGE IIIB                         5                           5
  STAGE IIIC                         1                           0
  STAGE IV                           4                           0
[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                          T2 T3 T4
  DEL PEAK  7(3Q24) MUTATED    5 17 22
  DEL PEAK  7(3Q24) WILD-TYPE  9 15 12
D10V4, multiclass
    clus
vv   DEL PEAK  7(3Q24) MUTATED DEL PEAK  7(3Q24) WILD-TYPE
  T2                         5                           9
  T3                        17                          15
  T4                        22                          12
[1] 3 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  7(3Q24) MUTATED   26  4
  DEL PEAK  7(3Q24) WILD-TYPE 25  0
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3Q24) MUTATED     26    4
  DEL PEAK  7(3Q24) WILD-TYPE   25    0
   clus
vv  DEL PEAK  7(3Q24) MUTATED DEL PEAK  7(3Q24) WILD-TYPE
  0                        26                          25
  1                         4                           0
[1] 2 2
[1] FALSE
D10V6, binary
                             cls
clus                           0  1
  DEL PEAK  7(3Q24) MUTATED   19 25
  DEL PEAK  7(3Q24) WILD-TYPE 16 20
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3Q24) MUTATED     19   25
  DEL PEAK  7(3Q24) WILD-TYPE   16   20
        clus
vv       DEL PEAK  7(3Q24) MUTATED DEL PEAK  7(3Q24) WILD-TYPE
  FEMALE                        19                          16
  MALE                          25                          20
[1] 2 2
[1] FALSE

Clustering(11) Variable = DEL PEAK  8(3Q29) MUTATION ANALYSIS
D11V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  8(3Q29) MUTATED   32 12
  DEL PEAK  8(3Q29) WILD-TYPE 35  1
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                         44                          36 
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                         12                           1 
$`DEL PEAK  8(3Q29) MUTATED`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9ED TCGA-V4-A9EE 
        4.90         4.50        13.64        26.56        28.41        13.08 
TCGA-V4-A9EF TCGA-V4-A9EI TCGA-V4-A9EL TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES 
       27.09        13.22        23.44        19.53        14.96        37.81 
TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9F0 TCGA-V4-A9F1 
       23.31        27.48        30.05        24.00        24.10        21.73 
TCGA-V4-A9F3 TCGA-V4-A9F5 TCGA-V4-A9F8 TCGA-VD-A8K8 TCGA-VD-A8KA TCGA-VD-A8KD 
       22.03         6.67        19.63        16.87        37.28         3.75 
TCGA-VD-A8KF TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM 
        1.32         0.33         1.25         2.10        20.98         0.13 
TCGA-VD-A8KN TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8T TCGA-WC-A87Y 
        2.24         1.45         7.50         2.83         0.49        31.40 
TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9A TCGA-YZ-A980 
       11.31         7.92        10.13         2.70        14.89        52.64 
TCGA-YZ-A984 TCGA-YZ-A985 
       42.08        25.81 

$`DEL PEAK  8(3Q29) WILD-TYPE`
TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9EH 
        4.04        74.53        30.38        24.69        24.43        22.03 
TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9ET TCGA-V4-A9EY TCGA-V4-A9EZ 
       12.56        18.64        22.03        31.66        25.02        19.69 
TCGA-V4-A9F2 TCGA-V4-A9F4 TCGA-V4-A9F7 TCGA-VD-A8K7 TCGA-VD-A8K9 TCGA-VD-A8KB 
       12.20        20.22        32.28         0.10         0.46        35.31 
TCGA-VD-A8KE TCGA-VD-A8KG TCGA-VD-A8KJ TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8Q 
       26.99         0.66        31.59        26.14         0.20         0.23 
TCGA-VD-AA8R TCGA-VD-AA8S TCGA-WC-A87T TCGA-WC-A87U TCGA-WC-A87W TCGA-WC-A880 
        0.20        14.04        70.65        51.98        45.57        31.99 
TCGA-WC-A881 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-AA9E TCGA-YZ-A982 TCGA-YZ-A983 
       22.82         0.39        10.36        14.20        16.27        17.98 

  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                       0.13                        0.10 
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                      52.64                       74.53 
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                     14.925                      21.125 
[1] "0.1 - 52.6 (14.9)" "0.1 - 74.5 (21.1)"
[1] "hr=" "13" 
D11V2, continuous
                             vv
clus                          STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  DEL PEAK  8(3Q29) MUTATED           3        14         16          5
  DEL PEAK  8(3Q29) WILD-TYPE         9        13          9          5
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK  8(3Q29) MUTATED            1        4
  DEL PEAK  8(3Q29) WILD-TYPE          0        0
D11V3, multiclass
            clus
vv           DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE
  STAGE IIA                          3                           9
  STAGE IIB                         14                          13
  STAGE IIIA                        16                           9
  STAGE IIIB                         5                           5
  STAGE IIIC                         1                           0
  STAGE IV                           4                           0
[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                          T2 T3 T4
  DEL PEAK  8(3Q29) MUTATED    5 17 22
  DEL PEAK  8(3Q29) WILD-TYPE  9 15 12
D11V4, multiclass
    clus
vv   DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE
  T2                         5                           9
  T3                        17                          15
  T4                        22                          12
[1] 3 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  8(3Q29) MUTATED   26  4
  DEL PEAK  8(3Q29) WILD-TYPE 25  0
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(3Q29) MUTATED     26    4
  DEL PEAK  8(3Q29) WILD-TYPE   25    0
   clus
vv  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE
  0                        26                          25
  1                         4                           0
[1] 2 2
[1] FALSE
D11V6, binary
                             cls
clus                           0  1
  DEL PEAK  8(3Q29) MUTATED   19 25
  DEL PEAK  8(3Q29) WILD-TYPE 16 20
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(3Q29) MUTATED     19   25
  DEL PEAK  8(3Q29) WILD-TYPE   16   20
        clus
vv       DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE
  FEMALE                        19                          16
  MALE                          25                          20
[1] 2 2
[1] FALSE

Clustering(12) Variable = DEL PEAK  9(5Q23.1) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(5Q23.1) MUTATED    4  0
  DEL PEAK  9(5Q23.1) WILD-TYPE 63 13
  DEL PEAK  9(5Q23.1) MUTATED DEL PEAK  9(5Q23.1) WILD-TYPE 
                            4                            76 
  DEL PEAK  9(5Q23.1) MUTATED DEL PEAK  9(5Q23.1) WILD-TYPE 
                            0                            13 
$`DEL PEAK  9(5Q23.1) MUTATED`
TCGA-V4-A9EA TCGA-VD-AA8P TCGA-WC-A87W TCGA-YZ-A982 
       24.69         2.83        45.57        16.27 

$`DEL PEAK  9(5Q23.1) WILD-TYPE`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 
        4.90         4.50         4.04        74.53        13.64        26.56 
TCGA-V4-A9E9 TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH 
       30.38        24.43        28.41        13.08        27.09        22.03 
TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EL TCGA-V4-A9EM TCGA-V4-A9EO 
       13.22        12.56        18.64        23.44        22.03        19.53 
TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW 
       14.96        37.81        31.66        23.31        27.48        30.05 
TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 
       24.00        25.02        19.69        24.10        21.73        12.20 
TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 
       22.03        20.22         6.67        32.28        19.63         0.10 
TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE 
       16.87         0.46        37.28        35.31         3.75        26.99 
TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK 
        1.32         0.66         0.33         1.25        31.59         2.10 
TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N 
       20.98         0.13         2.24        26.14         0.20         1.45 
TCGA-VD-AA8O TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T 
        7.50         0.23         0.20        14.04         0.49        70.65 
TCGA-WC-A87U TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A881 TCGA-WC-A882 TCGA-WC-A883 
       51.98        31.40        31.99        22.82        11.31         7.92 
TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9A TCGA-WC-AA9E 
        0.39        10.36        10.13         2.70        14.89        14.20 
TCGA-YZ-A980 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       52.64        17.98        42.08        25.81 

  DEL PEAK  9(5Q23.1) MUTATED DEL PEAK  9(5Q23.1) WILD-TYPE 
                         2.83                          0.10 
  DEL PEAK  9(5Q23.1) MUTATED DEL PEAK  9(5Q23.1) WILD-TYPE 
                        45.57                         74.53 
  DEL PEAK  9(5Q23.1) MUTATED DEL PEAK  9(5Q23.1) WILD-TYPE 
                       20.480                        19.085 
[1] "2.8 - 45.6 (20.5)" "0.1 - 74.5 (19.1)"
[1] "hr="     "7.2e+07"
D12V2, continuous
                               vv
clus                            STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  DEL PEAK  9(5Q23.1) MUTATED           1         1          1          1
  DEL PEAK  9(5Q23.1) WILD-TYPE        11        26         24          9
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  9(5Q23.1) MUTATED            0        0
  DEL PEAK  9(5Q23.1) WILD-TYPE          1        4
D12V3, multiclass
            clus
vv           DEL PEAK  9(5Q23.1) MUTATED DEL PEAK  9(5Q23.1) WILD-TYPE
  STAGE IIA                            1                            11
  STAGE IIB                            1                            26
  STAGE IIIA                           1                            24
  STAGE IIIB                           1                             9
  STAGE IIIC                           0                             1
  STAGE IV                             0                             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                            T2 T3 T4
  DEL PEAK  9(5Q23.1) MUTATED    1  1  2
  DEL PEAK  9(5Q23.1) WILD-TYPE 13 31 32
D12V4, multiclass
    clus
vv   DEL PEAK  9(5Q23.1) MUTATED DEL PEAK  9(5Q23.1) WILD-TYPE
  T2                           1                            13
  T3                           1                            31
  T4                           2                            32
[1] 3 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  9(5Q23.1) MUTATED    3  0
  DEL PEAK  9(5Q23.1) WILD-TYPE 48  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q23.1) MUTATED      3    0
  DEL PEAK  9(5Q23.1) WILD-TYPE   48    4
   clus
vv  DEL PEAK  9(5Q23.1) MUTATED DEL PEAK  9(5Q23.1) WILD-TYPE
  0                           3                            48
  1                           0                             4
[1] 2 2
[1] FALSE
D12V6, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q23.1) MUTATED    3  1
  DEL PEAK  9(5Q23.1) WILD-TYPE 32 44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q23.1) MUTATED      3    1
  DEL PEAK  9(5Q23.1) WILD-TYPE   32   44
        clus
vv       DEL PEAK  9(5Q23.1) MUTATED DEL PEAK  9(5Q23.1) WILD-TYPE
  FEMALE                           3                            32
  MALE                             1                            44
[1] 2 2
[1] FALSE

Clustering(13) Variable = DEL PEAK 10(6Q22.31) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 10(6Q22.31) MUTATED   19  5
  DEL PEAK 10(6Q22.31) WILD-TYPE 48  8
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                            24                             56 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                             5                              8 
$`DEL PEAK 10(6Q22.31) MUTATED`
TCGA-V3-A9ZX TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EI TCGA-V4-A9EL 
        4.50        13.64        26.56        30.38        13.22        23.44 
TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EZ TCGA-V4-A9F0 
       31.66        23.31        30.05        24.00        19.69        24.10 
TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-VD-A8K9 TCGA-VD-A8KB TCGA-VD-A8KI 
       22.03        20.22         6.67         0.46        35.31         1.25 
TCGA-VD-A8KJ TCGA-VD-A8KN TCGA-VD-AA8N TCGA-WC-A881 TCGA-WC-A88A TCGA-WC-AA9E 
       31.59         2.24         1.45        22.82         2.70        14.20 

$`DEL PEAK 10(6Q22.31) WILD-TYPE`
TCGA-RZ-AB0B TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9ED 
        4.90         4.04        74.53        24.69        24.43        28.41 
TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM 
       13.08        27.09        22.03        12.56        18.64        22.03 
TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9EV TCGA-V4-A9EY TCGA-V4-A9F1 
       19.53        14.96        37.81        27.48        25.02        21.73 
TCGA-V4-A9F2 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8KA 
       12.20        32.28        19.63         0.10        16.87        37.28 
TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KK 
        3.75        26.99         1.32         0.66         0.33         2.10 
TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8O TCGA-VD-AA8P 
       20.98         0.13        26.14         0.20         7.50         2.83 
TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87U 
        0.23         0.20        14.04         0.49        70.65        51.98 
TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 
       45.57        31.40        31.99        11.31         7.92         0.39 
TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-AA9A TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 
       10.36        10.13        14.89        52.64        16.27        17.98 
TCGA-YZ-A984 TCGA-YZ-A985 
       42.08        25.81 

  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                          0.46                           0.10 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                         35.31                          74.53 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                        21.125                         17.425 
[1] "0.5 - 35.3 (21.1)" "0.1 - 74.5 (17.4)"
[1] "hr=" "1.6"
D13V2, continuous
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  DEL PEAK 10(6Q22.31) MUTATED           3         7          8          3
  DEL PEAK 10(6Q22.31) WILD-TYPE         9        20         17          7
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 10(6Q22.31) MUTATED            1        2
  DEL PEAK 10(6Q22.31) WILD-TYPE          0        2
D13V3, multiclass
            clus
vv           DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  STAGE IIA                             3                              9
  STAGE IIB                             7                             20
  STAGE IIIA                            8                             17
  STAGE IIIB                            3                              7
  STAGE IIIC                            1                              0
  STAGE IV                              2                              2
[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                             T2 T3 T4
  DEL PEAK 10(6Q22.31) MUTATED    4  6 14
  DEL PEAK 10(6Q22.31) WILD-TYPE 10 26 20
D13V4, multiclass
    clus
vv   DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  T2                            4                             10
  T3                            6                             26
  T4                           14                             20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V5, binary
                                cls
clus                              0  1
  DEL PEAK 10(6Q22.31) MUTATED   15  2
  DEL PEAK 10(6Q22.31) WILD-TYPE 36  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.31) MUTATED     15    2
  DEL PEAK 10(6Q22.31) WILD-TYPE   36    2
   clus
vv  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  0                           15                             36
  1                            2                              2
[1] 2 2
[1] FALSE
D13V6, binary
                                cls
clus                              0  1
  DEL PEAK 10(6Q22.31) MUTATED    9 15
  DEL PEAK 10(6Q22.31) WILD-TYPE 26 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.31) MUTATED      9   15
  DEL PEAK 10(6Q22.31) WILD-TYPE   26   30
        clus
vv       DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  FEMALE                            9                             26
  MALE                             15                             30
[1] 2 2
[1] FALSE

Clustering(14) Variable = DEL PEAK 11(6Q27) MUTATION ANALYSIS
D14V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 11(6Q27) MUTATED   18  6
  DEL PEAK 11(6Q27) WILD-TYPE 49  7
  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                         24                          56 
  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                          6                           7 
$`DEL PEAK 11(6Q27) MUTATED`
TCGA-V3-A9ZX TCGA-V4-A9E7 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EE TCGA-V4-A9EI 
        4.50        13.64        26.56        30.38        13.08        13.22 
TCGA-V4-A9EL TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EZ 
       23.44        31.66        23.31        30.05        24.00        19.69 
TCGA-V4-A9F0 TCGA-V4-A9F3 TCGA-V4-A9F5 TCGA-VD-A8K9 TCGA-VD-A8KB TCGA-VD-A8KI 
       24.10        22.03         6.67         0.46        35.31         1.25 
TCGA-VD-A8KJ TCGA-VD-A8KN TCGA-VD-AA8N TCGA-WC-A881 TCGA-WC-A88A TCGA-WC-AA9E 
       31.59         2.24         1.45        22.82         2.70        14.20 

$`DEL PEAK 11(6Q27) WILD-TYPE`
TCGA-RZ-AB0B TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9ED 
        4.90         4.04        74.53        24.69        24.43        28.41 
TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO 
       27.09        22.03        12.56        18.64        22.03        19.53 
TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9EV TCGA-V4-A9EY TCGA-V4-A9F1 TCGA-V4-A9F2 
       14.96        37.81        27.48        25.02        21.73        12.20 
TCGA-V4-A9F4 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8KA 
       20.22        32.28        19.63         0.10        16.87        37.28 
TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KK 
        3.75        26.99         1.32         0.66         0.33         2.10 
TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8O TCGA-VD-AA8P 
       20.98         0.13        26.14         0.20         7.50         2.83 
TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87U 
        0.23         0.20        14.04         0.49        70.65        51.98 
TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 
       45.57        31.40        31.99        11.31         7.92         0.39 
TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-AA9A TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 
       10.36        10.13        14.89        52.64        16.27        17.98 
TCGA-YZ-A984 TCGA-YZ-A985 
       42.08        25.81 

  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                       0.46                        0.10 
  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                      35.31                       74.53 
  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                      20.86                       18.31 
[1] "0.5 - 35.3 (20.9)" "0.1 - 74.5 (18.3)"
[1] "hr=" "2.3"
D14V2, continuous
                             vv
clus                          STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  DEL PEAK 11(6Q27) MUTATED           3         8          7          3
  DEL PEAK 11(6Q27) WILD-TYPE         9        19         18          7
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK 11(6Q27) MUTATED            1        2
  DEL PEAK 11(6Q27) WILD-TYPE          0        2
D14V3, multiclass
            clus
vv           DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE
  STAGE IIA                          3                           9
  STAGE IIB                          8                          19
  STAGE IIIA                         7                          18
  STAGE IIIB                         3                           7
  STAGE IIIC                         1                           0
  STAGE IV                           2                           2
[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                          T2 T3 T4
  DEL PEAK 11(6Q27) MUTATED    4  7 13
  DEL PEAK 11(6Q27) WILD-TYPE 10 25 21
D14V4, multiclass
    clus
vv   DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE
  T2                         4                          10
  T3                         7                          25
  T4                        13                          21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                             cls
clus                           0  1
  DEL PEAK 11(6Q27) MUTATED   15  2
  DEL PEAK 11(6Q27) WILD-TYPE 36  2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q27) MUTATED     15    2
  DEL PEAK 11(6Q27) WILD-TYPE   36    2
   clus
vv  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE
  0                        15                          36
  1                         2                           2
[1] 2 2
[1] FALSE
D14V6, binary
                             cls
clus                           0  1
  DEL PEAK 11(6Q27) MUTATED    9 15
  DEL PEAK 11(6Q27) WILD-TYPE 26 30
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q27) MUTATED      9   15
  DEL PEAK 11(6Q27) WILD-TYPE   26   30
        clus
vv       DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE
  FEMALE                         9                          26
  MALE                          15                          30
[1] 2 2
[1] FALSE

Clustering(15) Variable = DEL PEAK 12(8P11.22) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 12(8P11.22) MUTATED   14  5
  DEL PEAK 12(8P11.22) WILD-TYPE 53  8
  DEL PEAK 12(8P11.22) MUTATED DEL PEAK 12(8P11.22) WILD-TYPE 
                            19                             61 
  DEL PEAK 12(8P11.22) MUTATED DEL PEAK 12(8P11.22) WILD-TYPE 
                             5                              8 
$`DEL PEAK 12(8P11.22) MUTATED`
TCGA-V3-A9ZX TCGA-V4-A9E7 TCGA-V4-A9EI TCGA-V4-A9EL TCGA-V4-A9EU TCGA-V4-A9EX 
        4.50        13.64        13.22        23.44        23.31        24.00 
TCGA-V4-A9F1 TCGA-V4-A9F3 TCGA-V4-A9F5 TCGA-VD-A8K8 TCGA-VD-A8KF TCGA-VD-A8KI 
       21.73        22.03         6.67        16.87         1.32         1.25 
TCGA-VD-A8KJ TCGA-VD-A8KM TCGA-VD-AA8N TCGA-WC-A87Y TCGA-WC-A888 TCGA-WC-A88A 
       31.59         0.13         1.45        31.40        10.13         2.70 
TCGA-YZ-A980 
       52.64 

$`DEL PEAK 12(8P11.22) WILD-TYPE`
TCGA-RZ-AB0B TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA 
        4.90         4.04        74.53        26.56        30.38        24.69 
TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EJ 
       24.43        28.41        13.08        27.09        22.03        12.56 
TCGA-V4-A9EK TCGA-V4-A9EM TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET 
       18.64        22.03        19.53        14.96        37.81        31.66 
TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F2 
       27.48        30.05        25.02        19.69        24.10        12.20 
TCGA-V4-A9F4 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K9 TCGA-VD-A8KA 
       20.22        32.28        19.63         0.10         0.46        37.28 
TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KK 
       35.31         3.75        26.99         0.66         0.33         2.10 
TCGA-VD-A8KL TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8O TCGA-VD-AA8P 
       20.98         2.24        26.14         0.20         7.50         2.83 
TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87U 
        0.23         0.20        14.04         0.49        70.65        51.98 
TCGA-WC-A87W TCGA-WC-A880 TCGA-WC-A881 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A884 
       45.57        31.99        22.82        11.31         7.92         0.39 
TCGA-WC-A885 TCGA-WC-AA9A TCGA-WC-AA9E TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 
       10.36        14.89        14.20        16.27        17.98        42.08 
TCGA-YZ-A985 
       25.81 

  DEL PEAK 12(8P11.22) MUTATED DEL PEAK 12(8P11.22) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 12(8P11.22) MUTATED DEL PEAK 12(8P11.22) WILD-TYPE 
                         52.64                          74.53 
  DEL PEAK 12(8P11.22) MUTATED DEL PEAK 12(8P11.22) WILD-TYPE 
                         13.64                          19.63 
[1] "0.1 - 52.6 (13.6)" "0.1 - 74.5 (19.6)"
[1] "hr=" "2.4"
D15V2, continuous
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  DEL PEAK 12(8P11.22) MUTATED           0         8          5          2
  DEL PEAK 12(8P11.22) WILD-TYPE        12        19         20          8
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 12(8P11.22) MUTATED            1        2
  DEL PEAK 12(8P11.22) WILD-TYPE          0        2
D15V3, multiclass
            clus
vv           DEL PEAK 12(8P11.22) MUTATED DEL PEAK 12(8P11.22) WILD-TYPE
  STAGE IIA                             0                             12
  STAGE IIB                             8                             19
  STAGE IIIA                            5                             20
  STAGE IIIB                            2                              8
  STAGE IIIC                            1                              0
  STAGE IV                              2                              2
[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                             T2 T3 T4
  DEL PEAK 12(8P11.22) MUTATED    1  9  9
  DEL PEAK 12(8P11.22) WILD-TYPE 13 23 25
D15V4, multiclass
    clus
vv   DEL PEAK 12(8P11.22) MUTATED DEL PEAK 12(8P11.22) WILD-TYPE
  T2                            1                             13
  T3                            9                             23
  T4                            9                             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V5, binary
                                cls
clus                              0  1
  DEL PEAK 12(8P11.22) MUTATED   10  2
  DEL PEAK 12(8P11.22) WILD-TYPE 41  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(8P11.22) MUTATED     10    2
  DEL PEAK 12(8P11.22) WILD-TYPE   41    2
   clus
vv  DEL PEAK 12(8P11.22) MUTATED DEL PEAK 12(8P11.22) WILD-TYPE
  0                           10                             41
  1                            2                              2
[1] 2 2
[1] FALSE
D15V6, binary
                                cls
clus                              0  1
  DEL PEAK 12(8P11.22) MUTATED    6 13
  DEL PEAK 12(8P11.22) WILD-TYPE 29 32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(8P11.22) MUTATED      6   13
  DEL PEAK 12(8P11.22) WILD-TYPE   29   32
        clus
vv       DEL PEAK 12(8P11.22) MUTATED DEL PEAK 12(8P11.22) WILD-TYPE
  FEMALE                            6                             29
  MALE                             13                             32
[1] 2 2
[1] FALSE

Clustering(16) Variable = DEL PEAK 15(11Q24.3) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 15(11Q24.3) MUTATED    7  0
  DEL PEAK 15(11Q24.3) WILD-TYPE 60 13
  DEL PEAK 15(11Q24.3) MUTATED DEL PEAK 15(11Q24.3) WILD-TYPE 
                             7                             73 
  DEL PEAK 15(11Q24.3) MUTATED DEL PEAK 15(11Q24.3) WILD-TYPE 
                             0                             13 
$`DEL PEAK 15(11Q24.3) MUTATED`
TCGA-V4-A9EA TCGA-V4-A9F4 TCGA-VD-A8KB TCGA-VD-A8KG TCGA-WC-A880 TCGA-WC-A884 
       24.69        20.22        35.31         0.66        31.99         0.39 
TCGA-YZ-A984 
       42.08 

$`DEL PEAK 15(11Q24.3) WILD-TYPE`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 
        4.90         4.50         4.04        74.53        13.64        26.56 
TCGA-V4-A9E9 TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH 
       30.38        24.43        28.41        13.08        27.09        22.03 
TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EL TCGA-V4-A9EM TCGA-V4-A9EO 
       13.22        12.56        18.64        23.44        22.03        19.53 
TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV TCGA-V4-A9EW 
       14.96        37.81        31.66        23.31        27.48        30.05 
TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 
       24.00        25.02        19.69        24.10        21.73        12.20 
TCGA-V4-A9F3 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 
       22.03         6.67        32.28        19.63         0.10        16.87 
TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KH 
        0.46        37.28         3.75        26.99         1.32         0.33 
TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN 
        1.25        31.59         2.10        20.98         0.13         2.24 
TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8N TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q 
       26.14         0.20         1.45         7.50         2.83         0.23 
TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87U TCGA-WC-A87W 
        0.20        14.04         0.49        70.65        51.98        45.57 
TCGA-WC-A87Y TCGA-WC-A881 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A885 TCGA-WC-A888 
       31.40        22.82        11.31         7.92        10.36        10.13 
TCGA-WC-A88A TCGA-WC-AA9A TCGA-WC-AA9E TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 
        2.70        14.89        14.20        52.64        16.27        17.98 
TCGA-YZ-A985 
       25.81 

  DEL PEAK 15(11Q24.3) MUTATED DEL PEAK 15(11Q24.3) WILD-TYPE 
                          0.39                           0.10 
  DEL PEAK 15(11Q24.3) MUTATED DEL PEAK 15(11Q24.3) WILD-TYPE 
                         42.08                          74.53 
  DEL PEAK 15(11Q24.3) MUTATED DEL PEAK 15(11Q24.3) WILD-TYPE 
                         24.69                          17.98 
[1] "0.4 - 42.1 (24.7)" "0.1 - 74.5 (18.0)"
[1] "hr="     "7.8e+07"
D16V2, continuous
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  DEL PEAK 15(11Q24.3) MUTATED           1         2          3          1
  DEL PEAK 15(11Q24.3) WILD-TYPE        11        25         22          9
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 15(11Q24.3) MUTATED            0        0
  DEL PEAK 15(11Q24.3) WILD-TYPE          1        4
D16V3, multiclass
            clus
vv           DEL PEAK 15(11Q24.3) MUTATED DEL PEAK 15(11Q24.3) WILD-TYPE
  STAGE IIA                             1                             11
  STAGE IIB                             2                             25
  STAGE IIIA                            3                             22
  STAGE IIIB                            1                              9
  STAGE IIIC                            0                              1
  STAGE IV                              0                              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                             T2 T3 T4
  DEL PEAK 15(11Q24.3) MUTATED    1  2  4
  DEL PEAK 15(11Q24.3) WILD-TYPE 13 30 30
D16V4, multiclass
    clus
vv   DEL PEAK 15(11Q24.3) MUTATED DEL PEAK 15(11Q24.3) WILD-TYPE
  T2                            1                             13
  T3                            2                             30
  T4                            4                             30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V5, binary
                                cls
clus                              0  1
  DEL PEAK 15(11Q24.3) MUTATED    4  0
  DEL PEAK 15(11Q24.3) WILD-TYPE 47  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q24.3) MUTATED      4    0
  DEL PEAK 15(11Q24.3) WILD-TYPE   47    4
   clus
vv  DEL PEAK 15(11Q24.3) MUTATED DEL PEAK 15(11Q24.3) WILD-TYPE
  0                            4                             47
  1                            0                              4
[1] 2 2
[1] FALSE
D16V6, binary
                                cls
clus                              0  1
  DEL PEAK 15(11Q24.3) MUTATED    4  3
  DEL PEAK 15(11Q24.3) WILD-TYPE 31 42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q24.3) MUTATED      4    3
  DEL PEAK 15(11Q24.3) WILD-TYPE   31   42
        clus
vv       DEL PEAK 15(11Q24.3) MUTATED DEL PEAK 15(11Q24.3) WILD-TYPE
  FEMALE                            4                             31
  MALE                              3                             42
[1] 2 2
[1] FALSE

Clustering(17) Variable = DEL PEAK 16(16Q12.1) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 16(16Q12.1) MUTATED   10  6
  DEL PEAK 16(16Q12.1) WILD-TYPE 57  7
  DEL PEAK 16(16Q12.1) MUTATED DEL PEAK 16(16Q12.1) WILD-TYPE 
                            16                             64 
  DEL PEAK 16(16Q12.1) MUTATED DEL PEAK 16(16Q12.1) WILD-TYPE 
                             6                              7 
$`DEL PEAK 16(16Q12.1) MUTATED`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9EI TCGA-V4-A9EL 
        4.90         4.50        74.53        13.64        13.22        23.44 
TCGA-V4-A9EQ TCGA-V4-A9EU TCGA-V4-A9EZ TCGA-VD-A8KM TCGA-VD-AA8N TCGA-WC-A881 
       14.96        23.31        19.69         0.13         1.45        22.82 
TCGA-WC-A884 TCGA-WC-A88A TCGA-WC-AA9A TCGA-WC-AA9E 
        0.39         2.70        14.89        14.20 

$`DEL PEAK 16(16Q12.1) WILD-TYPE`
TCGA-V3-A9ZY TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9ED 
        4.04        26.56        30.38        24.69        24.43        28.41 
TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM 
       13.08        27.09        22.03        12.56        18.64        22.03 
TCGA-V4-A9EO TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX 
       19.53        37.81        31.66        27.48        30.05        24.00 
TCGA-V4-A9EY TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 
       25.02        24.10        21.73        12.20        22.03        20.22 
TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 
        6.67        32.28        19.63         0.10        16.87         0.46 
TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG 
       37.28        35.31         3.75        26.99         1.32         0.66 
TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KN 
        0.33         1.25        31.59         2.10        20.98         2.24 
TCGA-VD-A8KO TCGA-VD-AA8M TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R 
       26.14         0.20         7.50         2.83         0.23         0.20 
TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87U TCGA-WC-A87W TCGA-WC-A87Y 
       14.04         0.49        70.65        51.98        45.57        31.40 
TCGA-WC-A880 TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A885 TCGA-WC-A888 TCGA-YZ-A980 
       31.99        11.31         7.92        10.36        10.13        52.64 
TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       16.27        17.98        42.08        25.81 

  DEL PEAK 16(16Q12.1) MUTATED DEL PEAK 16(16Q12.1) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 16(16Q12.1) MUTATED DEL PEAK 16(16Q12.1) WILD-TYPE 
                         74.53                          70.65 
  DEL PEAK 16(16Q12.1) MUTATED DEL PEAK 16(16Q12.1) WILD-TYPE 
                         13.92                          20.60 
[1] "0.1 - 74.5 (13.9)" "0.1 - 70.7 (20.6)"
[1] "hr=" "4.6"
D17V2, continuous
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  DEL PEAK 16(16Q12.1) MUTATED           2         5          3          3
  DEL PEAK 16(16Q12.1) WILD-TYPE        10        22         22          7
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 16(16Q12.1) MUTATED            1        2
  DEL PEAK 16(16Q12.1) WILD-TYPE          0        2
D17V3, multiclass
            clus
vv           DEL PEAK 16(16Q12.1) MUTATED DEL PEAK 16(16Q12.1) WILD-TYPE
  STAGE IIA                             2                             10
  STAGE IIB                             5                             22
  STAGE IIIA                            3                             22
  STAGE IIIB                            3                              7
  STAGE IIIC                            1                              0
  STAGE IV                              2                              2
[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                             T2 T3 T4
  DEL PEAK 16(16Q12.1) MUTATED    3  4  9
  DEL PEAK 16(16Q12.1) WILD-TYPE 11 28 25
D17V4, multiclass
    clus
vv   DEL PEAK 16(16Q12.1) MUTATED DEL PEAK 16(16Q12.1) WILD-TYPE
  T2                            3                             11
  T3                            4                             28
  T4                            9                             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V5, binary
                                cls
clus                              0  1
  DEL PEAK 16(16Q12.1) MUTATED   10  2
  DEL PEAK 16(16Q12.1) WILD-TYPE 41  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(16Q12.1) MUTATED     10    2
  DEL PEAK 16(16Q12.1) WILD-TYPE   41    2
   clus
vv  DEL PEAK 16(16Q12.1) MUTATED DEL PEAK 16(16Q12.1) WILD-TYPE
  0                           10                             41
  1                            2                              2
[1] 2 2
[1] FALSE
D17V6, binary
                                cls
clus                              0  1
  DEL PEAK 16(16Q12.1) MUTATED    6 10
  DEL PEAK 16(16Q12.1) WILD-TYPE 29 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(16Q12.1) MUTATED      6   10
  DEL PEAK 16(16Q12.1) WILD-TYPE   29   35
        clus
vv       DEL PEAK 16(16Q12.1) MUTATED DEL PEAK 16(16Q12.1) WILD-TYPE
  FEMALE                            6                             29
  MALE                             10                             35
[1] 2 2
[1] FALSE

Clustering(18) Variable = DEL PEAK 17(16Q23.3) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 17(16Q23.3) MUTATED   11  6
  DEL PEAK 17(16Q23.3) WILD-TYPE 56  7
  DEL PEAK 17(16Q23.3) MUTATED DEL PEAK 17(16Q23.3) WILD-TYPE 
                            17                             63 
  DEL PEAK 17(16Q23.3) MUTATED DEL PEAK 17(16Q23.3) WILD-TYPE 
                             6                              7 
$`DEL PEAK 17(16Q23.3) MUTATED`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9EI TCGA-V4-A9EL 
        4.90         4.50        74.53        13.64        13.22        23.44 
TCGA-V4-A9EQ TCGA-V4-A9EU TCGA-V4-A9EZ TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-AA8N 
       14.96        23.31        19.69         0.13         2.24         1.45 
TCGA-WC-A881 TCGA-WC-A884 TCGA-WC-A88A TCGA-WC-AA9A TCGA-WC-AA9E 
       22.82         0.39         2.70        14.89        14.20 

$`DEL PEAK 17(16Q23.3) WILD-TYPE`
TCGA-V3-A9ZY TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9ED 
        4.04        26.56        30.38        24.69        24.43        28.41 
TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM 
       13.08        27.09        22.03        12.56        18.64        22.03 
TCGA-V4-A9EO TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX 
       19.53        37.81        31.66        27.48        30.05        24.00 
TCGA-V4-A9EY TCGA-V4-A9F0 TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 
       25.02        24.10        21.73        12.20        22.03        20.22 
TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 
        6.67        32.28        19.63         0.10        16.87         0.46 
TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG 
       37.28        35.31         3.75        26.99         1.32         0.66 
TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KO 
        0.33         1.25        31.59         2.10        20.98        26.14 
TCGA-VD-AA8M TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S 
        0.20         7.50         2.83         0.23         0.20        14.04 
TCGA-VD-AA8T TCGA-WC-A87T TCGA-WC-A87U TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 
        0.49        70.65        51.98        45.57        31.40        31.99 
TCGA-WC-A882 TCGA-WC-A883 TCGA-WC-A885 TCGA-WC-A888 TCGA-YZ-A980 TCGA-YZ-A982 
       11.31         7.92        10.36        10.13        52.64        16.27 
TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       17.98        42.08        25.81 

  DEL PEAK 17(16Q23.3) MUTATED DEL PEAK 17(16Q23.3) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 17(16Q23.3) MUTATED DEL PEAK 17(16Q23.3) WILD-TYPE 
                         74.53                          70.65 
  DEL PEAK 17(16Q23.3) MUTATED DEL PEAK 17(16Q23.3) WILD-TYPE 
                         13.64                          20.98 
[1] "0.1 - 74.5 (13.6)" "0.1 - 70.7 (21.0)"
[1] "hr=" "4.6"
D18V2, continuous
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  DEL PEAK 17(16Q23.3) MUTATED           3         5          3          3
  DEL PEAK 17(16Q23.3) WILD-TYPE         9        22         22          7
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 17(16Q23.3) MUTATED            1        2
  DEL PEAK 17(16Q23.3) WILD-TYPE          0        2
D18V3, multiclass
            clus
vv           DEL PEAK 17(16Q23.3) MUTATED DEL PEAK 17(16Q23.3) WILD-TYPE
  STAGE IIA                             3                              9
  STAGE IIB                             5                             22
  STAGE IIIA                            3                             22
  STAGE IIIB                            3                              7
  STAGE IIIC                            1                              0
  STAGE IV                              2                              2
[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                             T2 T3 T4
  DEL PEAK 17(16Q23.3) MUTATED    4  4  9
  DEL PEAK 17(16Q23.3) WILD-TYPE 10 28 25
D18V4, multiclass
    clus
vv   DEL PEAK 17(16Q23.3) MUTATED DEL PEAK 17(16Q23.3) WILD-TYPE
  T2                            4                             10
  T3                            4                             28
  T4                            9                             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V5, binary
                                cls
clus                              0  1
  DEL PEAK 17(16Q23.3) MUTATED   10  2
  DEL PEAK 17(16Q23.3) WILD-TYPE 41  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(16Q23.3) MUTATED     10    2
  DEL PEAK 17(16Q23.3) WILD-TYPE   41    2
   clus
vv  DEL PEAK 17(16Q23.3) MUTATED DEL PEAK 17(16Q23.3) WILD-TYPE
  0                           10                             41
  1                            2                              2
[1] 2 2
[1] FALSE
D18V6, binary
                                cls
clus                              0  1
  DEL PEAK 17(16Q23.3) MUTATED    7 10
  DEL PEAK 17(16Q23.3) WILD-TYPE 28 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(16Q23.3) MUTATED      7   10
  DEL PEAK 17(16Q23.3) WILD-TYPE   28   35
        clus
vv       DEL PEAK 17(16Q23.3) MUTATED DEL PEAK 17(16Q23.3) WILD-TYPE
  FEMALE                            7                             28
  MALE                             10                             35
[1] 2 2
[1] FALSE

Clustering(19) Variable = DEL PEAK 18(16Q24.3) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(16Q24.3) MUTATED   11  6
  DEL PEAK 18(16Q24.3) WILD-TYPE 56  7
  DEL PEAK 18(16Q24.3) MUTATED DEL PEAK 18(16Q24.3) WILD-TYPE 
                            17                             63 
  DEL PEAK 18(16Q24.3) MUTATED DEL PEAK 18(16Q24.3) WILD-TYPE 
                             6                              7 
$`DEL PEAK 18(16Q24.3) MUTATED`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9EI TCGA-V4-A9EL 
        4.90         4.50        74.53        13.64        13.22        23.44 
TCGA-V4-A9EQ TCGA-V4-A9EU TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-VD-A8KM TCGA-VD-A8KN 
       14.96        23.31        19.69        24.10         0.13         2.24 
TCGA-VD-AA8N TCGA-WC-A881 TCGA-WC-A88A TCGA-WC-AA9A TCGA-WC-AA9E 
        1.45        22.82         2.70        14.89        14.20 

$`DEL PEAK 18(16Q24.3) WILD-TYPE`
TCGA-V3-A9ZY TCGA-V4-A9E8 TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9ED 
        4.04        26.56        30.38        24.69        24.43        28.41 
TCGA-V4-A9EE TCGA-V4-A9EF TCGA-V4-A9EH TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EM 
       13.08        27.09        22.03        12.56        18.64        22.03 
TCGA-V4-A9EO TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EV TCGA-V4-A9EW TCGA-V4-A9EX 
       19.53        37.81        31.66        27.48        30.05        24.00 
TCGA-V4-A9EY TCGA-V4-A9F1 TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 
       25.02        21.73        12.20        22.03        20.22         6.67 
TCGA-V4-A9F7 TCGA-V4-A9F8 TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA 
       32.28        19.63         0.10        16.87         0.46        37.28 
TCGA-VD-A8KB TCGA-VD-A8KD TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH 
       35.31         3.75        26.99         1.32         0.66         0.33 
TCGA-VD-A8KI TCGA-VD-A8KJ TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KO TCGA-VD-AA8M 
        1.25        31.59         2.10        20.98        26.14         0.20 
TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8Q TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T 
        7.50         2.83         0.23         0.20        14.04         0.49 
TCGA-WC-A87T TCGA-WC-A87U TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A882 
       70.65        51.98        45.57        31.40        31.99        11.31 
TCGA-WC-A883 TCGA-WC-A884 TCGA-WC-A885 TCGA-WC-A888 TCGA-YZ-A980 TCGA-YZ-A982 
        7.92         0.39        10.36        10.13        52.64        16.27 
TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       17.98        42.08        25.81 

  DEL PEAK 18(16Q24.3) MUTATED DEL PEAK 18(16Q24.3) WILD-TYPE 
                          0.13                           0.10 
  DEL PEAK 18(16Q24.3) MUTATED DEL PEAK 18(16Q24.3) WILD-TYPE 
                         74.53                          70.65 
  DEL PEAK 18(16Q24.3) MUTATED DEL PEAK 18(16Q24.3) WILD-TYPE 
                         14.20                          20.22 
[1] "0.1 - 74.5 (14.2)" "0.1 - 70.7 (20.2)"
[1] "hr=" "4"  
D19V2, continuous
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  DEL PEAK 18(16Q24.3) MUTATED           3         5          3          3
  DEL PEAK 18(16Q24.3) WILD-TYPE         9        22         22          7
                                vv
clus                             STAGE IIIC STAGE IV
  DEL PEAK 18(16Q24.3) MUTATED            1        2
  DEL PEAK 18(16Q24.3) WILD-TYPE          0        2
D19V3, multiclass
            clus
vv           DEL PEAK 18(16Q24.3) MUTATED DEL PEAK 18(16Q24.3) WILD-TYPE
  STAGE IIA                             3                              9
  STAGE IIB                             5                             22
  STAGE IIIA                            3                             22
  STAGE IIIB                            3                              7
  STAGE IIIC                            1                              0
  STAGE IV                              2                              2
[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                             T2 T3 T4
  DEL PEAK 18(16Q24.3) MUTATED    4  4  9
  DEL PEAK 18(16Q24.3) WILD-TYPE 10 28 25
D19V4, multiclass
    clus
vv   DEL PEAK 18(16Q24.3) MUTATED DEL PEAK 18(16Q24.3) WILD-TYPE
  T2                            4                             10
  T3                            4                             28
  T4                            9                             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V5, binary
                                cls
clus                              0  1
  DEL PEAK 18(16Q24.3) MUTATED   10  2
  DEL PEAK 18(16Q24.3) WILD-TYPE 41  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(16Q24.3) MUTATED     10    2
  DEL PEAK 18(16Q24.3) WILD-TYPE   41    2
   clus
vv  DEL PEAK 18(16Q24.3) MUTATED DEL PEAK 18(16Q24.3) WILD-TYPE
  0                           10                             41
  1                            2                              2
[1] 2 2
[1] FALSE
D19V6, binary
                                cls
clus                              0  1
  DEL PEAK 18(16Q24.3) MUTATED    6 11
  DEL PEAK 18(16Q24.3) WILD-TYPE 29 34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(16Q24.3) MUTATED      6   11
  DEL PEAK 18(16Q24.3) WILD-TYPE   29   34
        clus
vv       DEL PEAK 18(16Q24.3) MUTATED DEL PEAK 18(16Q24.3) WILD-TYPE
  FEMALE                            6                             29
  MALE                             11                             34
[1] 2 2
[1] FALSE

Clustering(20) Variable = DEL PEAK 19(17Q12) MUTATION ANALYSIS
D20V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 19(17Q12) MUTATED    3  0
  DEL PEAK 19(17Q12) WILD-TYPE 64 13
  DEL PEAK 19(17Q12) MUTATED DEL PEAK 19(17Q12) WILD-TYPE 
                           3                           77 
  DEL PEAK 19(17Q12) MUTATED DEL PEAK 19(17Q12) WILD-TYPE 
                           0                           13 
$`DEL PEAK 19(17Q12) MUTATED`
TCGA-VD-AA8M TCGA-VD-AA8Q TCGA-WC-A884 
        0.20         0.23         0.39 

$`DEL PEAK 19(17Q12) WILD-TYPE`
TCGA-RZ-AB0B TCGA-V3-A9ZX TCGA-V3-A9ZY TCGA-V4-A9E5 TCGA-V4-A9E7 TCGA-V4-A9E8 
        4.90         4.50         4.04        74.53        13.64        26.56 
TCGA-V4-A9E9 TCGA-V4-A9EA TCGA-V4-A9EC TCGA-V4-A9ED TCGA-V4-A9EE TCGA-V4-A9EF 
       30.38        24.69        24.43        28.41        13.08        27.09 
TCGA-V4-A9EH TCGA-V4-A9EI TCGA-V4-A9EJ TCGA-V4-A9EK TCGA-V4-A9EL TCGA-V4-A9EM 
       22.03        13.22        12.56        18.64        23.44        22.03 
TCGA-V4-A9EO TCGA-V4-A9EQ TCGA-V4-A9ES TCGA-V4-A9ET TCGA-V4-A9EU TCGA-V4-A9EV 
       19.53        14.96        37.81        31.66        23.31        27.48 
TCGA-V4-A9EW TCGA-V4-A9EX TCGA-V4-A9EY TCGA-V4-A9EZ TCGA-V4-A9F0 TCGA-V4-A9F1 
       30.05        24.00        25.02        19.69        24.10        21.73 
TCGA-V4-A9F2 TCGA-V4-A9F3 TCGA-V4-A9F4 TCGA-V4-A9F5 TCGA-V4-A9F7 TCGA-V4-A9F8 
       12.20        22.03        20.22         6.67        32.28        19.63 
TCGA-VD-A8K7 TCGA-VD-A8K8 TCGA-VD-A8K9 TCGA-VD-A8KA TCGA-VD-A8KB TCGA-VD-A8KD 
        0.10        16.87         0.46        37.28        35.31         3.75 
TCGA-VD-A8KE TCGA-VD-A8KF TCGA-VD-A8KG TCGA-VD-A8KH TCGA-VD-A8KI TCGA-VD-A8KJ 
       26.99         1.32         0.66         0.33         1.25        31.59 
TCGA-VD-A8KK TCGA-VD-A8KL TCGA-VD-A8KM TCGA-VD-A8KN TCGA-VD-A8KO TCGA-VD-AA8N 
        2.10        20.98         0.13         2.24        26.14         1.45 
TCGA-VD-AA8O TCGA-VD-AA8P TCGA-VD-AA8R TCGA-VD-AA8S TCGA-VD-AA8T TCGA-WC-A87T 
        7.50         2.83         0.20        14.04         0.49        70.65 
TCGA-WC-A87U TCGA-WC-A87W TCGA-WC-A87Y TCGA-WC-A880 TCGA-WC-A881 TCGA-WC-A882 
       51.98        45.57        31.40        31.99        22.82        11.31 
TCGA-WC-A883 TCGA-WC-A885 TCGA-WC-A888 TCGA-WC-A88A TCGA-WC-AA9A TCGA-WC-AA9E 
        7.92        10.36        10.13         2.70        14.89        14.20 
TCGA-YZ-A980 TCGA-YZ-A982 TCGA-YZ-A983 TCGA-YZ-A984 TCGA-YZ-A985 
       52.64        16.27        17.98        42.08        25.81 

  DEL PEAK 19(17Q12) MUTATED DEL PEAK 19(17Q12) WILD-TYPE 
                         0.2                          0.1 
  DEL PEAK 19(17Q12) MUTATED DEL PEAK 19(17Q12) WILD-TYPE 
                        0.39                        74.53 
  DEL PEAK 19(17Q12) MUTATED DEL PEAK 19(17Q12) WILD-TYPE 
                        0.23                        19.63 
[1] "0.2 - 0.4 (0.2)"   "0.1 - 74.5 (19.6)"
[1] "hr=" "3.1"
D20V2, continuous
                              vv
clus                           STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  DEL PEAK 19(17Q12) MUTATED           1         1          0          1
  DEL PEAK 19(17Q12) WILD-TYPE        11        26         25          9
                              vv
clus                           STAGE IIIC STAGE IV
  DEL PEAK 19(17Q12) MUTATED            0        0
  DEL PEAK 19(17Q12) WILD-TYPE          1        4
D20V3, multiclass
            clus
vv           DEL PEAK 19(17Q12) MUTATED DEL PEAK 19(17Q12) WILD-TYPE
  STAGE IIA                           1                           11
  STAGE IIB                           1                           26
  STAGE IIIA                          0                           25
  STAGE IIIB                          1                            9
  STAGE IIIC                          0                            1
  STAGE IV                            0                            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                           T2 T3 T4
  DEL PEAK 19(17Q12) MUTATED    1  1  1
  DEL PEAK 19(17Q12) WILD-TYPE 13 31 33
D20V4, multiclass
    clus
vv   DEL PEAK 19(17Q12) MUTATED DEL PEAK 19(17Q12) WILD-TYPE
  T2                          1                           13
  T3                          1                           31
  T4                          1                           33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V5, binary
                              cls
clus                            0  1
  DEL PEAK 19(17Q12) MUTATED    3  0
  DEL PEAK 19(17Q12) WILD-TYPE 48  4
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(17Q12) MUTATED      3    0
  DEL PEAK 19(17Q12) WILD-TYPE   48    4
   clus
vv  DEL PEAK 19(17Q12) MUTATED DEL PEAK 19(17Q12) WILD-TYPE
  0                          3                           48
  1                          0                            4
[1] 2 2
[1] FALSE
D20V6, binary
                              cls
clus                            0  1
  DEL PEAK 19(17Q12) MUTATED    1  2
  DEL PEAK 19(17Q12) WILD-TYPE 34 43
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(17Q12) MUTATED      1    2
  DEL PEAK 19(17Q12) WILD-TYPE   34   43
        clus
vv       DEL PEAK 19(17Q12) MUTATED DEL PEAK 19(17Q12) WILD-TYPE
  FEMALE                          1                           34
  MALE                            2                           43
[1] 2 2
[1] FALSE
