[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTMESO-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/MESO-TP/11541580/MESO-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/MESO-TP/11544692/transformed.cor.cli.txt"

nPatients in clinical file=39, in cluster file=87, common to both=39
[1] 21 39
[1] "DEL PEAK  1(1P36.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            18                             21 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            18                             21 
[1] "DEL PEAK  2(1P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                           18                            21 
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                           18                            21 
[1] "DEL PEAK  3(2Q35) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                          7                          32 
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                          7                          32 
[1] "DEL PEAK  4(3P21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                           25                            14 
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                           25                            14 
[1] "DEL PEAK  5(4Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                         20                          19 
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                         20                          19 
[1] "DEL PEAK  6(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           22                            17 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           22                            17 
[1] "DEL PEAK  7(5Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE 
                            8                            31 
  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE 
                            8                            31 
[1] "DEL PEAK  8(6Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE 
                           20                            19 
  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE 
                           20                            19 
[1] "DEL PEAK  9(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                         17                          22 
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                         17                          22 
[1] "DEL PEAK 10(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                            7                            32 
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                            7                            32 
[1] "DEL PEAK 11(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                           25                            14 
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                           25                            14 
[1] "DEL PEAK 12(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                            13                             26 
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                            13                             26 
[1] "DEL PEAK 13(10Q25.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                            16                             23 
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                            16                             23 
[1] "DEL PEAK 14(11Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE 
                             8                             31 
  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE 
                             8                             31 
[1] "DEL PEAK 15(12P13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE 
                              6                              33 
  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE 
                              6                              33 
[1] "DEL PEAK 16(13Q14.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE 
                             23                              16 
  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE 
                             23                              16 
[1] "DEL PEAK 17(14Q32.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE 
                             19                              20 
  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE 
                             19                              20 
[1] "DEL PEAK 18(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE 
                            14                             25 
  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE 
                            14                             25 
[1] "DEL PEAK 19(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                             5                             34 
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                             5                             34 
[1] "DEL PEAK 20(16Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE 
                            13                             26 
  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE 
                            13                             26 
[1] "DEL PEAK 21(22Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE 
                            32                              7 
  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE 
                            32                              7 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "NEOPLASM.DISEASESTAGE"                 
 [6] "PATHOLOGY.T.STAGE"                     
 [7] "PATHOLOGY.N.STAGE"                     
 [8] "PATHOLOGY.M.STAGE"                     
 [9] "DCCUPLOADDATE"                         
[10] "GENDER"                                
[11] "RADIATIONTHERAPY"                      
[12] "KARNOFSKYPERFORMANCESCORE"             
[13] "RADIATIONS.RADIATION.REGIMENINDICATION"
[14] "RACE"                                  
[15] "ETHNICITY"                             
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 39 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
          NA           NA           NA           NA           NA           NA 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
         371           49          108           NA           NA           NA 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
          NA           NA           NA           NA           NA           NA 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
        1316         1575          414            7           NA          200 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 
          NA           NA           NA          256           NA           NA 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G 
          NA           NA          723          652           NA           NA 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
          NA           NA           NA 
Variable 1:'AGE':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RACE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "PATHOLOGY.M.STAGE"     "GENDER"               
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 39 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=23, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 7 17 13  2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
    7    17    15 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 7 17 13  2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
    7    17    15 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
25  6  5 
[1] "table(vv)"
vv
N0 N1 N2 
25  6  5 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
25  6  5 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
25  6  5 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = DEL PEAK  1(1P36.31) MUTATION ANALYSIS
D1V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.31) MUTATED    5 13
  DEL PEAK  1(1P36.31) WILD-TYPE  5 16
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            18                             21 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            13                             16 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
        5.52         8.02         6.08         1.87        12.20         1.61 
TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-SC-A6LN 
        3.55        18.81         5.19        10.95        13.61         6.58 
TCGA-SH-A7BC TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88E TCGA-XT-AASU 
       23.90        23.64        14.99        13.35        14.27         4.67 

$`DEL PEAK  1(1P36.31) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LP 
       17.95        31.20        80.84        91.73        23.31        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM 
        3.52        24.89        43.27        51.78         0.23        28.96 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UT-A88C TCGA-UT-A88D 
       15.09         7.99         8.42         6.48        23.77        21.44 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-YS-AA4M 
        2.50         4.73         2.76 

  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                          1.61                           0.23 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                         23.90                          91.73 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                         9.485                         17.950 
[1] "1.6 - 23.9 (9.5)"  "0.2 - 91.7 (17.9)"
[1] "hr=" "2.3"
D1V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  1(1P36.31) MUTATED         1        1        0        6        10
  DEL PEAK  1(1P36.31) WILD-TYPE       2        0        1        5         9
                                vv
clus                             STAGE IV
  DEL PEAK  1(1P36.31) MUTATED          0
  DEL PEAK  1(1P36.31) WILD-TYPE        4
D1V3, multiclass
           clus
vv          DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  STAGE I                              1                              2
  STAGE IA                             1                              0
  STAGE IB                             0                              1
  STAGE II                             6                              5
  STAGE III                           10                              9
  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                             T1 T2 T3+T4
  DEL PEAK  1(1P36.31) MUTATED    2  8     8
  DEL PEAK  1(1P36.31) WILD-TYPE  5  9     7
D1V4, multiclass
       clus
vv      DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  T1                               2                              5
  T2                               8                              9
  T3+T4                            8                              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK  1(1P36.31) MUTATED   12  2  3
  DEL PEAK  1(1P36.31) WILD-TYPE 13  4  2
D1V5, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  N0                           12                             13
  N1                            2                              4
  N2                            3                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK  1(1P36.31) MUTATED   16  0  2
  DEL PEAK  1(1P36.31) WILD-TYPE 15  2  4
D1V6, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  M0                           16                             15
  M1                            0                              2
  MX                            2                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.31) MUTATED    5 13
  DEL PEAK  1(1P36.31) WILD-TYPE  5 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      5   13
  DEL PEAK  1(1P36.31) WILD-TYPE    5   16
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  FEMALE                            5                              5
  MALE                             13                             16
[1] 2 2
[1] FALSE

Clustering(2) Variable = DEL PEAK  2(1P21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(1P21.3) MUTATED    6 12
  DEL PEAK  2(1P21.3) WILD-TYPE  4 17
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                           18                            21 
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                           12                            17 
$`DEL PEAK  2(1P21.3) MUTATED`
TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LC 
        5.52         6.08         1.87         1.61         3.55        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-SC-A6LM 
       18.81        23.31        17.33        10.95        13.61        28.96 
TCGA-SC-A6LN TCGA-SH-A7BD TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC7 TCGA-UT-A88D 
        6.58        15.09         8.42         6.48        13.35        21.44 

$`DEL PEAK  2(1P21.3) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LM 
       17.95         8.02        31.20        12.20        80.84         5.19 
TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SH-A7BC 
        3.52        24.89        43.27        51.78         0.23        23.90 
TCGA-SH-A7BH TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G 
        7.99        23.64        14.99        23.77        14.27         2.50 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
        4.73         4.67         2.76 

  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                         1.61                          0.23 
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                        91.73                         80.84 
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                        12.15                         14.27 
[1] "1.6 - 91.7 (12.1)" "0.2 - 80.8 (14.3)"
[1] "hr=" "1.1"
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  2(1P21.3) MUTATED         0        1        0        8         7
  DEL PEAK  2(1P21.3) WILD-TYPE       3        0        1        3        12
                               vv
clus                            STAGE IV
  DEL PEAK  2(1P21.3) MUTATED          2
  DEL PEAK  2(1P21.3) WILD-TYPE        2
D2V3, multiclass
           clus
vv          DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE
  STAGE I                             0                             3
  STAGE IA                            1                             0
  STAGE IB                            0                             1
  STAGE II                            8                             3
  STAGE III                           7                            12
  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                            T1 T2 T3+T4
  DEL PEAK  2(1P21.3) MUTATED    1 11     6
  DEL PEAK  2(1P21.3) WILD-TYPE  6  6     9
D2V4, multiclass
       clus
vv      DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE
  T1                              1                             6
  T2                             11                             6
  T3+T4                           6                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  2(1P21.3) MUTATED   13  3  1
  DEL PEAK  2(1P21.3) WILD-TYPE 12  3  4
D2V5, multiclass
    clus
vv   DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE
  N0                          13                            12
  N1                           3                             3
  N2                           1                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  DEL PEAK  2(1P21.3) MUTATED   16  1  1
  DEL PEAK  2(1P21.3) WILD-TYPE 15  1  5
D2V6, multiclass
    clus
vv   DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE
  M0                          16                            15
  M1                           1                             1
  MX                           1                             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P21.3) MUTATED    5 13
  DEL PEAK  2(1P21.3) WILD-TYPE  5 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P21.3) MUTATED      5   13
  DEL PEAK  2(1P21.3) WILD-TYPE    5   16
        clus
vv       DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE
  FEMALE                           5                             5
  MALE                            13                            16
[1] 2 2
[1] FALSE

Clustering(3) Variable = DEL PEAK  3(2Q35) MUTATION ANALYSIS
D3V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  3(2Q35) MUTATED    1  6
  DEL PEAK  3(2Q35) WILD-TYPE  9 23
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                          7                          32 
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                          6                          23 
$`DEL PEAK  3(2Q35) MUTATED`
TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4LI TCGA-SH-A7BH 
        5.52         6.08         1.87        12.20        18.81         7.99 
TCGA-UD-AAC7 
       13.35 

$`DEL PEAK  3(2Q35) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX 
       17.95         8.02        31.20         1.61         3.55        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       91.73        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM 
       24.89        43.27        51.78        13.61         0.23        28.96 
TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 
        6.58        23.90        15.09         8.42         6.48        23.64 
TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
       14.99        23.77        21.44        14.27         2.50         4.73 
TCGA-XT-AASU TCGA-YS-AA4M 
        4.67         2.76 

  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                       1.87                        0.23 
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                      18.81                       91.73 
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                       7.99                       14.63 
[1] "1.9 - 18.8 (8.0)"  "0.2 - 91.7 (14.6)"
[1] "hr=" "2.6"
D3V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  3(2Q35) MUTATED         0        1        0        2         4
  DEL PEAK  3(2Q35) WILD-TYPE       3        0        1        9        15
                             vv
clus                          STAGE IV
  DEL PEAK  3(2Q35) MUTATED          0
  DEL PEAK  3(2Q35) WILD-TYPE        4
D3V3, multiclass
           clus
vv          DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  STAGE I                           0                           3
  STAGE IA                          1                           0
  STAGE IB                          0                           1
  STAGE II                          2                           9
  STAGE III                         4                          15
  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                          T1 T2 T3+T4
  DEL PEAK  3(2Q35) MUTATED    1  2     4
  DEL PEAK  3(2Q35) WILD-TYPE  6 15    11
D3V4, multiclass
       clus
vv      DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  T1                            1                           6
  T2                            2                          15
  T3+T4                         4                          11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2
  DEL PEAK  3(2Q35) MUTATED    7  0  0
  DEL PEAK  3(2Q35) WILD-TYPE 18  6  5
D3V5, multiclass
    clus
vv   DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  N0                         7                          18
  N1                         0                           6
  N2                         0                           5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          M0 M1 MX
  DEL PEAK  3(2Q35) MUTATED    7  0  0
  DEL PEAK  3(2Q35) WILD-TYPE 24  2  6
D3V6, multiclass
    clus
vv   DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  M0                         7                          24
  M1                         0                           2
  MX                         0                           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"
D3V7, binary
                             cls
clus                           0  1
  DEL PEAK  3(2Q35) MUTATED    5  2
  DEL PEAK  3(2Q35) WILD-TYPE  5 27
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(2Q35) MUTATED      5    2
  DEL PEAK  3(2Q35) WILD-TYPE    5   27
        clus
vv       DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  FEMALE                         5                           5
  MALE                           2                          27
[1] 2 2
[1] FALSE

Clustering(4) Variable = DEL PEAK  4(3P21.1) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(3P21.1) MUTATED    5 20
  DEL PEAK  4(3P21.1) WILD-TYPE  5  9
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                           25                            14 
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                           20                             9 
$`DEL PEAK  4(3P21.1) MUTATED`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 
       17.95         8.02         1.87        12.20         1.61         3.55 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       80.84        91.73         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SH-A7BC TCGA-SH-A7BD 
       24.89        13.61         0.23        28.96        23.90        15.09 
TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E 
        6.48        23.64        14.99        13.35        23.77        14.27 
TCGA-XT-AASU 
        4.67 

$`DEL PEAK  4(3P21.1) WILD-TYPE`
TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-LK-A4O4 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BQ 
        5.52         6.08        31.20        18.81        23.31        43.27 
TCGA-MQ-A6BR TCGA-SC-A6LN TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UT-A88D TCGA-UT-A88G 
       51.78         6.58         7.99         8.42        21.44         2.50 
TCGA-UT-A97Y TCGA-YS-AA4M 
        4.73         2.76 

  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                         0.23                          2.50 
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                        91.73                         51.78 
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                       13.610                         8.205 
[1] "0.2 - 91.7 (13.6)" "2.5 - 51.8 (8.2)" 
[1] "hr=" "1.2"
D4V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  4(3P21.1) MUTATED         2        0        1        7        12
  DEL PEAK  4(3P21.1) WILD-TYPE       1        1        0        4         7
                               vv
clus                            STAGE IV
  DEL PEAK  4(3P21.1) MUTATED          3
  DEL PEAK  4(3P21.1) WILD-TYPE        1
D4V3, multiclass
           clus
vv          DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  STAGE I                             2                             1
  STAGE IA                            0                             1
  STAGE IB                            1                             0
  STAGE II                            7                             4
  STAGE III                          12                             7
  STAGE IV                            3                             1
[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                            T1 T2 T3+T4
  DEL PEAK  4(3P21.1) MUTATED    3 10    12
  DEL PEAK  4(3P21.1) WILD-TYPE  4  7     3
D4V4, multiclass
       clus
vv      DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  T1                              3                             4
  T2                             10                             7
  T3+T4                          12                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  4(3P21.1) MUTATED   15  3  4
  DEL PEAK  4(3P21.1) WILD-TYPE 10  3  1
D4V5, multiclass
    clus
vv   DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  N0                          15                            10
  N1                           3                             3
  N2                           4                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  DEL PEAK  4(3P21.1) MUTATED   20  1  4
  DEL PEAK  4(3P21.1) WILD-TYPE 11  1  2
D4V6, multiclass
    clus
vv   DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  M0                          20                            11
  M1                           1                             1
  MX                           4                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                               cls
clus                             0  1
  DEL PEAK  4(3P21.1) MUTATED    5 20
  DEL PEAK  4(3P21.1) WILD-TYPE  5  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P21.1) MUTATED      5   20
  DEL PEAK  4(3P21.1) WILD-TYPE    5    9
        clus
vv       DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  FEMALE                           5                             5
  MALE                            20                             9
[1] 2 2
[1] FALSE

Clustering(5) Variable = DEL PEAK  5(4Q26) MUTATION ANALYSIS
D5V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  5(4Q26) MUTATED    7 13
  DEL PEAK  5(4Q26) WILD-TYPE  3 16
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                         20                          19 
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                         13                          16 
$`DEL PEAK  5(4Q26) MUTATED`
TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LI 
        6.08         1.87        12.20         1.61         3.55        18.81 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BR TCGA-MQ-A6BS 
        5.19        17.33         3.52        10.95        51.78        13.61 
TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC7 
        6.58        23.90         7.99         8.42         6.48        13.35 
TCGA-UT-A88G TCGA-UT-A97Y 
        2.50         4.73 

$`DEL PEAK  5(4Q26) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       17.95         5.52         8.02        31.20        80.84        91.73 
TCGA-MQ-A4LJ TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SH-A7BD 
       23.31        24.89        43.27         0.23        28.96        15.09 
TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-XT-AASU 
       23.64        14.99        23.77        21.44        14.27         4.67 
TCGA-YS-AA4M 
        2.76 

  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                       1.61                        0.23 
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                      51.78                       91.73 
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                      7.285                      21.440 
[1] "1.6 - 51.8 (7.3)"  "0.2 - 91.7 (21.4)"
[1] "hr=" "1.9"
D5V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  5(4Q26) MUTATED         1        1        0        6        12
  DEL PEAK  5(4Q26) WILD-TYPE       2        0        1        5         7
                             vv
clus                          STAGE IV
  DEL PEAK  5(4Q26) MUTATED          0
  DEL PEAK  5(4Q26) WILD-TYPE        4
D5V3, multiclass
           clus
vv          DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  STAGE I                           1                           2
  STAGE IA                          1                           0
  STAGE IB                          0                           1
  STAGE II                          6                           5
  STAGE III                        12                           7
  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                          T1 T2 T3+T4
  DEL PEAK  5(4Q26) MUTATED    3  7    10
  DEL PEAK  5(4Q26) WILD-TYPE  4 10     5
D5V4, multiclass
       clus
vv      DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  T1                            3                           4
  T2                            7                          10
  T3+T4                        10                           5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2
  DEL PEAK  5(4Q26) MUTATED   15  3  2
  DEL PEAK  5(4Q26) WILD-TYPE 10  3  3
D5V5, multiclass
    clus
vv   DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  N0                        15                          10
  N1                         3                           3
  N2                         2                           3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          M0 M1 MX
  DEL PEAK  5(4Q26) MUTATED   18  0  2
  DEL PEAK  5(4Q26) WILD-TYPE 13  2  4
D5V6, multiclass
    clus
vv   DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  M0                        18                          13
  M1                         0                           2
  MX                         2                           4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                             cls
clus                           0  1
  DEL PEAK  5(4Q26) MUTATED    7 13
  DEL PEAK  5(4Q26) WILD-TYPE  3 16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(4Q26) MUTATED      7   13
  DEL PEAK  5(4Q26) WILD-TYPE    3   16
        clus
vv       DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  FEMALE                         7                           3
  MALE                          13                          16
[1] 2 2
[1] FALSE

Clustering(6) Variable = DEL PEAK  6(4Q34.3) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(4Q34.3) MUTATED    7 15
  DEL PEAK  6(4Q34.3) WILD-TYPE  3 14
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           22                            17 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           15                            14 
$`DEL PEAK  6(4Q34.3) MUTATED`
TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LI 
        5.52         6.08        12.20         1.61         3.55        18.81 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LN 
        5.19        17.33        10.95        51.78        13.61         6.58 
TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 
       23.90         7.99         8.42         6.48        23.64        14.99 
TCGA-UD-AAC7 TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
       13.35        14.27         2.50         4.73 

$`DEL PEAK  6(4Q34.3) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       17.95         8.02         1.87        31.20        80.84        91.73 
TCGA-MQ-A4LJ TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-NQ-A57I TCGA-SC-A6LM 
       23.31         3.52        24.89        43.27         0.23        28.96 
TCGA-SH-A7BD TCGA-UT-A88C TCGA-UT-A88D TCGA-XT-AASU TCGA-YS-AA4M 
       15.09        23.77        21.44         4.67         2.76 

  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                         1.61                          0.23 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                        51.78                         91.73 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                        9.685                        21.440 
[1] "1.6 - 51.8 (9.7)"  "0.2 - 91.7 (21.4)"
[1] "hr=" "1.7"
D6V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  6(4Q34.3) MUTATED         2        1        0        7        12
  DEL PEAK  6(4Q34.3) WILD-TYPE       1        0        1        4         7
                               vv
clus                            STAGE IV
  DEL PEAK  6(4Q34.3) MUTATED          0
  DEL PEAK  6(4Q34.3) WILD-TYPE        4
D6V3, multiclass
           clus
vv          DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  STAGE I                             2                             1
  STAGE IA                            1                             0
  STAGE IB                            0                             1
  STAGE II                            7                             4
  STAGE III                          12                             7
  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                            T1 T2 T3+T4
  DEL PEAK  6(4Q34.3) MUTATED    4  9     9
  DEL PEAK  6(4Q34.3) WILD-TYPE  3  8     6
D6V4, multiclass
       clus
vv      DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  T1                              4                             3
  T2                              9                             8
  T3+T4                           9                             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"
                               vv
clus                            N0 N1 N2
  DEL PEAK  6(4Q34.3) MUTATED   16  3  3
  DEL PEAK  6(4Q34.3) WILD-TYPE  9  3  2
D6V5, multiclass
    clus
vv   DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  N0                          16                             9
  N1                           3                             3
  N2                           3                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  DEL PEAK  6(4Q34.3) MUTATED   20  0  2
  DEL PEAK  6(4Q34.3) WILD-TYPE 11  2  4
D6V6, multiclass
    clus
vv   DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  M0                          20                            11
  M1                           0                             2
  MX                           2                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q34.3) MUTATED    7 15
  DEL PEAK  6(4Q34.3) WILD-TYPE  3 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED      7   15
  DEL PEAK  6(4Q34.3) WILD-TYPE    3   14
        clus
vv       DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  FEMALE                           7                             3
  MALE                            15                            14
[1] 2 2
[1] FALSE

Clustering(7) Variable = DEL PEAK  7(5Q23.2) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  7(5Q23.2) MUTATED    3  5
  DEL PEAK  7(5Q23.2) WILD-TYPE  7 24
  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE 
                            8                            31 
  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE 
                            5                            24 
$`DEL PEAK  7(5Q23.2) MUTATED`
TCGA-LK-A4O7 TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SH-A7BD TCGA-UD-AABZ 
        3.55         3.52        13.61         6.58        15.09         6.48 
TCGA-UD-AAC7 TCGA-XT-AASU 
       13.35         4.67 

$`DEL PEAK  7(5Q23.2) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       17.95         5.52         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       12.20         1.61        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
        5.19        17.33        10.95        24.89        43.27        51.78 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AAC4 
        0.23        28.96        23.90         7.99         8.42        23.64 
TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
       14.99        23.77        21.44        14.27         2.50         4.73 
TCGA-YS-AA4M 
        2.76 

  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE 
                         3.52                          0.23 
  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE 
                        15.09                         91.73 
  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE 
                         6.53                         14.99 
[1] "3.5 - 15.1 (6.5)"  "0.2 - 91.7 (15.0)"
[1] "hr=" "2.1"
D7V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  7(5Q23.2) MUTATED         0        0        0        3         4
  DEL PEAK  7(5Q23.2) WILD-TYPE       3        1        1        8        15
                               vv
clus                            STAGE IV
  DEL PEAK  7(5Q23.2) MUTATED          1
  DEL PEAK  7(5Q23.2) WILD-TYPE        3
D7V3, multiclass
           clus
vv          DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE
  STAGE I                             0                             3
  STAGE IA                            0                             1
  STAGE IB                            0                             1
  STAGE II                            3                             8
  STAGE III                           4                            15
  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                            T1 T2 T3+T4
  DEL PEAK  7(5Q23.2) MUTATED    0  5     3
  DEL PEAK  7(5Q23.2) WILD-TYPE  7 12    12
D7V4, multiclass
       clus
vv      DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE
  T1                              0                             7
  T2                              5                            12
  T3+T4                           3                            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"
                               vv
clus                            N0 N1 N2
  DEL PEAK  7(5Q23.2) MUTATED    5  1  1
  DEL PEAK  7(5Q23.2) WILD-TYPE 20  5  4
D7V5, multiclass
    clus
vv   DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE
  N0                           5                            20
  N1                           1                             5
  N2                           1                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  DEL PEAK  7(5Q23.2) MUTATED    5  1  2
  DEL PEAK  7(5Q23.2) WILD-TYPE 26  1  4
D7V6, multiclass
    clus
vv   DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE
  M0                           5                            26
  M1                           1                             1
  MX                           2                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                               cls
clus                             0  1
  DEL PEAK  7(5Q23.2) MUTATED    0  8
  DEL PEAK  7(5Q23.2) WILD-TYPE 10 21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5Q23.2) MUTATED      0    8
  DEL PEAK  7(5Q23.2) WILD-TYPE   10   21
        clus
vv       DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE
  FEMALE                           0                            10
  MALE                             8                            21
[1] 2 2
[1] FALSE

Clustering(8) Variable = DEL PEAK  8(6Q22.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(6Q22.1) MUTATED    3 17
  DEL PEAK  8(6Q22.1) WILD-TYPE  7 12
  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE 
                           20                            19 
  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE 
                           17                            12 
$`DEL PEAK  8(6Q22.1) MUTATED`
TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        8.02         6.08         1.87         3.55        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       18.81         5.19         3.52        10.95        24.89        43.27 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BD TCGA-UD-AAC6 TCGA-UD-AAC7 
       13.61         0.23        23.90        15.09        14.99        13.35 
TCGA-UT-A88G TCGA-XT-AASU 
        2.50         4.67 

$`DEL PEAK  8(6Q22.1) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4LJ 
       17.95         5.52        31.20        12.20         1.61        23.31 
TCGA-MQ-A4LP TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BH TCGA-SH-A9CT 
       17.33        51.78        28.96         6.58         7.99         8.42 
TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y 
        6.48        23.64        23.77        21.44        14.27         4.73 
TCGA-YS-AA4M 
        2.76 

  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE 
                         0.23                          1.61 
  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE 
                        91.73                         51.78 
  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE 
                        12.15                         14.27 
[1] "0.2 - 91.7 (12.1)" "1.6 - 51.8 (14.3)"
[1] "hr=" "1.3"
D8V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  8(6Q22.1) MUTATED         1        1        1        8         8
  DEL PEAK  8(6Q22.1) WILD-TYPE       2        0        0        3        11
                               vv
clus                            STAGE IV
  DEL PEAK  8(6Q22.1) MUTATED          1
  DEL PEAK  8(6Q22.1) WILD-TYPE        3
D8V3, multiclass
           clus
vv          DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE
  STAGE I                             1                             2
  STAGE IA                            1                             0
  STAGE IB                            1                             0
  STAGE II                            8                             3
  STAGE III                           8                            11
  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                            T1 T2 T3+T4
  DEL PEAK  8(6Q22.1) MUTATED    3 10     7
  DEL PEAK  8(6Q22.1) WILD-TYPE  4  7     8
D8V4, multiclass
       clus
vv      DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE
  T1                              3                             4
  T2                             10                             7
  T3+T4                           7                             8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  8(6Q22.1) MUTATED   15  2  1
  DEL PEAK  8(6Q22.1) WILD-TYPE 10  4  4
D8V5, multiclass
    clus
vv   DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE
  N0                          15                            10
  N1                           2                             4
  N2                           1                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  DEL PEAK  8(6Q22.1) MUTATED   14  1  5
  DEL PEAK  8(6Q22.1) WILD-TYPE 17  1  1
D8V6, multiclass
    clus
vv   DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE
  M0                          14                            17
  M1                           1                             1
  MX                           5                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                               cls
clus                             0  1
  DEL PEAK  8(6Q22.1) MUTATED    3 17
  DEL PEAK  8(6Q22.1) WILD-TYPE  7 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(6Q22.1) MUTATED      3   17
  DEL PEAK  8(6Q22.1) WILD-TYPE    7   12
        clus
vv       DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE
  FEMALE                           3                             7
  MALE                            17                            12
[1] 2 2
[1] FALSE

Clustering(9) Variable = DEL PEAK  9(6Q26) MUTATION ANALYSIS
D9V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  9(6Q26) MUTATED    3 14
  DEL PEAK  9(6Q26) WILD-TYPE  7 15
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                         17                          22 
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                         14                          15 
$`DEL PEAK  9(6Q26) MUTATED`
TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
        5.52         6.08         1.87        80.84        91.73        18.81 
TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM 
        5.19        10.95        43.27        13.61         0.23        28.96 
TCGA-SC-A6LN TCGA-SH-A7BC TCGA-UD-AAC7 TCGA-UT-A88E TCGA-UT-A88G 
        6.58        23.90        13.35        14.27         2.50 

$`DEL PEAK  9(6Q26) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 
       17.95         8.02        31.20        12.20         1.61         3.55 
TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BR TCGA-SH-A7BD 
       23.31        17.33         3.52        24.89        51.78        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C 
        7.99         8.42         6.48        23.64        14.99        23.77 
TCGA-UT-A88D TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
       21.44         4.73         4.67         2.76 

  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                       0.23                        1.61 
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                      91.73                       51.78 
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                     13.350                      13.595 
[1] "0.2 - 91.7 (13.3)" "1.6 - 51.8 (13.6)"
[1] "hr=" "1"  
D9V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  9(6Q26) MUTATED         2        1        1        6         6
  DEL PEAK  9(6Q26) WILD-TYPE       1        0        0        5        13
                             vv
clus                          STAGE IV
  DEL PEAK  9(6Q26) MUTATED          1
  DEL PEAK  9(6Q26) WILD-TYPE        3
D9V3, multiclass
           clus
vv          DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  STAGE I                           2                           1
  STAGE IA                          1                           0
  STAGE IB                          1                           0
  STAGE II                          6                           5
  STAGE III                         6                          13
  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                          T1 T2 T3+T4
  DEL PEAK  9(6Q26) MUTATED    4  7     6
  DEL PEAK  9(6Q26) WILD-TYPE  3 10     9
D9V4, multiclass
       clus
vv      DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  T1                            4                           3
  T2                            7                          10
  T3+T4                         6                           9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2
  DEL PEAK  9(6Q26) MUTATED   13  0  2
  DEL PEAK  9(6Q26) WILD-TYPE 12  6  3
D9V5, multiclass
    clus
vv   DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  N0                        13                          12
  N1                         0                           6
  N2                         2                           3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          M0 M1 MX
  DEL PEAK  9(6Q26) MUTATED   14  0  3
  DEL PEAK  9(6Q26) WILD-TYPE 17  2  3
D9V6, multiclass
    clus
vv   DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  M0                        14                          17
  M1                         0                           2
  MX                         3                           3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                             cls
clus                           0  1
  DEL PEAK  9(6Q26) MUTATED    4 13
  DEL PEAK  9(6Q26) WILD-TYPE  6 16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(6Q26) MUTATED      4   13
  DEL PEAK  9(6Q26) WILD-TYPE    6   16
        clus
vv       DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  FEMALE                         4                           6
  MALE                          13                          16
[1] 2 2
[1] FALSE

Clustering(10) Variable = DEL PEAK 10(8P23.2) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 10(8P23.2) MUTATED    3  4
  DEL PEAK 10(8P23.2) WILD-TYPE  7 25
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                            7                            32 
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                            4                            25 
$`DEL PEAK 10(8P23.2) MUTATED`
TCGA-LK-A4O0 TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-SC-A6LN 
        6.08        91.73        18.81        43.27        13.61         6.58 
TCGA-UD-AAC4 
       23.64 

$`DEL PEAK 10(8P23.2) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
        1.61         3.55        80.84        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM 
        3.52        10.95        24.89        51.78         0.23        28.96 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC6 
       23.90        15.09         7.99         8.42         6.48        14.99 
TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
       13.35        23.77        21.44        14.27         2.50         4.73 
TCGA-XT-AASU TCGA-YS-AA4M 
        4.67         2.76 

  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                         6.08                          0.23 
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                        91.73                         80.84 
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                       18.810                        11.575 
[1] "6.1 - 91.7 (18.8)" "0.2 - 80.8 (11.6)"
[1] "hr=" "2.9"
D10V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 10(8P23.2) MUTATED         0        1        0        4         2
  DEL PEAK 10(8P23.2) WILD-TYPE       3        0        1        7        17
                               vv
clus                            STAGE IV
  DEL PEAK 10(8P23.2) MUTATED          0
  DEL PEAK 10(8P23.2) WILD-TYPE        4
D10V3, multiclass
           clus
vv          DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  STAGE I                             0                             3
  STAGE IA                            1                             0
  STAGE IB                            0                             1
  STAGE II                            4                             7
  STAGE III                           2                            17
  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                            T1 T2 T3+T4
  DEL PEAK 10(8P23.2) MUTATED    1  6     0
  DEL PEAK 10(8P23.2) WILD-TYPE  6 11    15
D10V4, multiclass
       clus
vv      DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  T1                              1                             6
  T2                              6                            11
  T3+T4                           0                            15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK 10(8P23.2) MUTATED    5  0  2
  DEL PEAK 10(8P23.2) WILD-TYPE 20  6  3
D10V5, multiclass
    clus
vv   DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  N0                           5                            20
  N1                           0                             6
  N2                           2                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  DEL PEAK 10(8P23.2) MUTATED    5  0  2
  DEL PEAK 10(8P23.2) WILD-TYPE 26  2  4
D10V6, multiclass
    clus
vv   DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  M0                           5                            26
  M1                           0                             2
  MX                           2                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                               cls
clus                             0  1
  DEL PEAK 10(8P23.2) MUTATED    1  6
  DEL PEAK 10(8P23.2) WILD-TYPE  9 23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(8P23.2) MUTATED      1    6
  DEL PEAK 10(8P23.2) WILD-TYPE    9   23
        clus
vv       DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  FEMALE                           1                             9
  MALE                             6                            23
[1] 2 2
[1] FALSE

Clustering(11) Variable = DEL PEAK 11(9P21.3) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 11(9P21.3) MUTATED    5 20
  DEL PEAK 11(9P21.3) WILD-TYPE  5  9
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                           25                            14 
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                           20                             9 
$`DEL PEAK 11(9P21.3) MUTATED`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O7 
       17.95         5.52         6.08         1.87        12.20         3.55 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL 
       18.81        23.31         5.19        17.33         3.52        10.95 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-UD-AABZ 
       13.61         0.23        28.96         6.58        23.90         6.48 
TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G 
       23.64        14.99        13.35        21.44        14.27         2.50 
TCGA-XT-AASU 
        4.67 

$`DEL PEAK 11(9P21.3) WILD-TYPE`
TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A6BN 
        8.02        31.20         1.61        80.84        91.73        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UT-A88C 
       43.27        51.78        15.09         7.99         8.42        23.77 
TCGA-UT-A97Y TCGA-YS-AA4M 
        4.73         2.76 

  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                         0.23                          1.61 
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                        28.96                         91.73 
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                        12.20                         19.43 
[1] "0.2 - 29.0 (12.2)" "1.6 - 91.7 (19.4)"
[1] "hr=" "3.5"
D11V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 11(9P21.3) MUTATED         1        1        1        7        13
  DEL PEAK 11(9P21.3) WILD-TYPE       2        0        0        4         6
                               vv
clus                            STAGE IV
  DEL PEAK 11(9P21.3) MUTATED          2
  DEL PEAK 11(9P21.3) WILD-TYPE        2
D11V3, multiclass
           clus
vv          DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  STAGE I                             1                             2
  STAGE IA                            1                             0
  STAGE IB                            1                             0
  STAGE II                            7                             4
  STAGE III                          13                             6
  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                            T1 T2 T3+T4
  DEL PEAK 11(9P21.3) MUTATED    3 10    12
  DEL PEAK 11(9P21.3) WILD-TYPE  4  7     3
D11V4, multiclass
       clus
vv      DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  T1                              3                             4
  T2                             10                             7
  T3+T4                          12                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK 11(9P21.3) MUTATED   16  2  4
  DEL PEAK 11(9P21.3) WILD-TYPE  9  4  1
D11V5, multiclass
    clus
vv   DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  N0                          16                             9
  N1                           2                             4
  N2                           4                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  DEL PEAK 11(9P21.3) MUTATED   22  0  3
  DEL PEAK 11(9P21.3) WILD-TYPE  9  2  3
D11V6, multiclass
    clus
vv   DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  M0                          22                             9
  M1                           0                             2
  MX                           3                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                               cls
clus                             0  1
  DEL PEAK 11(9P21.3) MUTATED    5 20
  DEL PEAK 11(9P21.3) WILD-TYPE  5  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(9P21.3) MUTATED      5   20
  DEL PEAK 11(9P21.3) WILD-TYPE    5    9
        clus
vv       DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  FEMALE                           5                             5
  MALE                            20                             9
[1] 2 2
[1] FALSE

Clustering(12) Variable = DEL PEAK 12(10P15.3) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 12(10P15.3) MUTATED    2 11
  DEL PEAK 12(10P15.3) WILD-TYPE  8 18
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                            13                             26 
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                            11                             18 
$`DEL PEAK 12(10P15.3) MUTATED`
TCGA-LK-A4NY TCGA-LK-A4O2 TCGA-LK-A4O7 TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
        5.52         1.87         3.55         5.19        17.33         3.52 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BH TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
       13.61         0.23         7.99        14.27         2.50         4.73 
TCGA-XT-AASU 
        4.67 

$`DEL PEAK 12(10P15.3) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 
       17.95         8.02         6.08        31.20        12.20         1.61 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BL TCGA-MQ-A6BN 
       80.84        91.73        18.81        23.31        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD 
       43.27        51.78        28.96         6.58        23.90        15.09 
TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
        8.42         6.48        23.64        14.99        13.35        23.77 
TCGA-UT-A88D TCGA-YS-AA4M 
       21.44         2.76 

  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                          0.23                           1.61 
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                         17.33                          91.73 
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                          4.73                          18.38 
[1] "0.2 - 17.3 (4.7)"  "1.6 - 91.7 (18.4)"
[1] "hr=" "6.9"
D12V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 12(10P15.3) MUTATED         2        0        1        1         9
  DEL PEAK 12(10P15.3) WILD-TYPE       1        1        0       10        10
                                vv
clus                             STAGE IV
  DEL PEAK 12(10P15.3) MUTATED          0
  DEL PEAK 12(10P15.3) WILD-TYPE        4
D12V3, multiclass
           clus
vv          DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE
  STAGE I                              2                              1
  STAGE IA                             0                              1
  STAGE IB                             1                              0
  STAGE II                             1                             10
  STAGE III                            9                             10
  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                             T1 T2 T3+T4
  DEL PEAK 12(10P15.3) MUTATED    3  1     9
  DEL PEAK 12(10P15.3) WILD-TYPE  4 16     6
D12V4, multiclass
       clus
vv      DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE
  T1                               3                              4
  T2                               1                             16
  T3+T4                            9                              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"
                                vv
clus                             N0 N1 N2
  DEL PEAK 12(10P15.3) MUTATED   10  1  0
  DEL PEAK 12(10P15.3) WILD-TYPE 15  5  5
D12V5, multiclass
    clus
vv   DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE
  N0                           10                             15
  N1                            1                              5
  N2                            0                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK 12(10P15.3) MUTATED   10  0  3
  DEL PEAK 12(10P15.3) WILD-TYPE 21  2  3
D12V6, multiclass
    clus
vv   DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE
  M0                           10                             21
  M1                            0                              2
  MX                            3                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                                cls
clus                              0  1
  DEL PEAK 12(10P15.3) MUTATED    4  9
  DEL PEAK 12(10P15.3) WILD-TYPE  6 20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(10P15.3) MUTATED      4    9
  DEL PEAK 12(10P15.3) WILD-TYPE    6   20
        clus
vv       DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE
  FEMALE                            4                              6
  MALE                              9                             20
[1] 2 2
[1] FALSE

Clustering(13) Variable = DEL PEAK 13(10Q25.2) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 13(10Q25.2) MUTATED    4 12
  DEL PEAK 13(10Q25.2) WILD-TYPE  6 17
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                            16                             23 
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                            12                             17 
$`DEL PEAK 13(10Q25.2) MUTATED`
TCGA-LK-A4NY TCGA-LK-A4O7 TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BS 
        5.52         3.55        17.33         3.52        24.89        13.61 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AAC7 
        0.23        28.96        15.09         7.99         8.42        13.35 
TCGA-UT-A88D TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       21.44         2.50         4.73         4.67 

$`DEL PEAK 13(10Q25.2) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         8.02         6.08         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
        1.61        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A6BL TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LN TCGA-SH-A7BC TCGA-UD-AABZ 
       10.95        43.27        51.78         6.58        23.90         6.48 
TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88E TCGA-YS-AA4M 
       23.64        14.99        23.77        14.27         2.76 

  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                          0.23                           1.61 
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                         28.96                          91.73 
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                         8.205                         14.990 
[1] "0.2 - 29.0 (8.2)"  "1.6 - 91.7 (15.0)"
[1] "hr=" "1.9"
D13V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 13(10Q25.2) MUTATED         1        0        1        4         8
  DEL PEAK 13(10Q25.2) WILD-TYPE       2        1        0        7        11
                                vv
clus                             STAGE IV
  DEL PEAK 13(10Q25.2) MUTATED          2
  DEL PEAK 13(10Q25.2) WILD-TYPE        2
D13V3, multiclass
           clus
vv          DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  STAGE I                              1                              2
  STAGE IA                             0                              1
  STAGE IB                             1                              0
  STAGE II                             4                              7
  STAGE III                            8                             11
  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                             T1 T2 T3+T4
  DEL PEAK 13(10Q25.2) MUTATED    2  6     8
  DEL PEAK 13(10Q25.2) WILD-TYPE  5 11     7
D13V4, multiclass
       clus
vv      DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  T1                               2                              5
  T2                               6                             11
  T3+T4                            8                              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 13(10Q25.2) MUTATED   11  2  0
  DEL PEAK 13(10Q25.2) WILD-TYPE 14  4  5
D13V5, multiclass
    clus
vv   DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  N0                           11                             14
  N1                            2                              4
  N2                            0                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK 13(10Q25.2) MUTATED   11  1  4
  DEL PEAK 13(10Q25.2) WILD-TYPE 20  1  2
D13V6, multiclass
    clus
vv   DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  M0                           11                             20
  M1                            1                              1
  MX                            4                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                                cls
clus                              0  1
  DEL PEAK 13(10Q25.2) MUTATED    5 11
  DEL PEAK 13(10Q25.2) WILD-TYPE  5 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q25.2) MUTATED      5   11
  DEL PEAK 13(10Q25.2) WILD-TYPE    5   18
        clus
vv       DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  FEMALE                            5                              5
  MALE                             11                             18
[1] 2 2
[1] FALSE

Clustering(14) Variable = DEL PEAK 14(11Q23.2) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 14(11Q23.2) MUTATED    2  6
  DEL PEAK 14(11Q23.2) WILD-TYPE  8 23
  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE 
                             8                             31 
  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE 
                             6                             23 
$`DEL PEAK 14(11Q23.2) MUTATED`
TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O7 TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-NQ-A57I 
       17.95         6.08         3.55         5.19         3.52         0.23 
TCGA-SH-A9CT TCGA-UD-AABZ 
        8.42         6.48 

$`DEL PEAK 14(11Q23.2) WILD-TYPE`
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 
        5.52         8.02         1.87        31.20        12.20         1.61 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A6BL 
       80.84        91.73        18.81        23.31        17.33        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN 
       24.89        43.27        51.78        13.61        28.96         6.58 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 
       23.90        15.09         7.99        23.64        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       23.77        21.44        14.27         2.50         4.73         4.67 
TCGA-YS-AA4M 
        2.76 

  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE 
                          0.23                           1.61 
  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE 
                         17.95                          91.73 
  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE 
                         5.635                         14.990 
[1] "0.2 - 17.9 (5.6)"  "1.6 - 91.7 (15.0)"
[1] "hr=" "3.3"
D14V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 14(11Q23.2) MUTATED         0        1        1        2         3
  DEL PEAK 14(11Q23.2) WILD-TYPE       3        0        0        9        16
                                vv
clus                             STAGE IV
  DEL PEAK 14(11Q23.2) MUTATED          1
  DEL PEAK 14(11Q23.2) WILD-TYPE        3
D14V3, multiclass
           clus
vv          DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE
  STAGE I                              0                              3
  STAGE IA                             1                              0
  STAGE IB                             1                              0
  STAGE II                             2                              9
  STAGE III                            3                             16
  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                             T1 T2 T3+T4
  DEL PEAK 14(11Q23.2) MUTATED    2  2     4
  DEL PEAK 14(11Q23.2) WILD-TYPE  5 15    11
D14V4, multiclass
       clus
vv      DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE
  T1                               2                              5
  T2                               2                             15
  T3+T4                            4                             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 14(11Q23.2) MUTATED    5  1  1
  DEL PEAK 14(11Q23.2) WILD-TYPE 20  5  4
D14V5, multiclass
    clus
vv   DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE
  N0                            5                             20
  N1                            1                              5
  N2                            1                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK 14(11Q23.2) MUTATED    7  0  1
  DEL PEAK 14(11Q23.2) WILD-TYPE 24  2  5
D14V6, multiclass
    clus
vv   DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE
  M0                            7                             24
  M1                            0                              2
  MX                            1                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                                cls
clus                              0  1
  DEL PEAK 14(11Q23.2) MUTATED    0  8
  DEL PEAK 14(11Q23.2) WILD-TYPE 10 21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q23.2) MUTATED      0    8
  DEL PEAK 14(11Q23.2) WILD-TYPE   10   21
        clus
vv       DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE
  FEMALE                            0                             10
  MALE                              8                             21
[1] 2 2
[1] FALSE

Clustering(15) Variable = DEL PEAK 15(12P13.31) MUTATION ANALYSIS
D15V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 15(12P13.31) MUTATED    2  4
  DEL PEAK 15(12P13.31) WILD-TYPE  8 25
  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE 
                              6                              33 
  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE 
                              4                              25 
$`DEL PEAK 15(12P13.31) MUTATED`
TCGA-LK-A4O7 TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AAC7 
        3.55         0.23        23.90         7.99         8.42        13.35 

$`DEL PEAK 15(12P13.31) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 
       17.95         5.52         8.02         6.08         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       12.20         1.61        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        5.19        17.33         3.52        10.95        24.89        43.27 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BD TCGA-UD-AABZ 
       51.78        13.61        28.96         6.58        15.09         6.48 
TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G 
       23.64        14.99        23.77        21.44        14.27         2.50 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-AA4M 
        4.73         4.67         2.76 

  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE 
                           0.23                            1.61 
  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE 
                          23.90                           91.73 
  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE 
                          8.205                          14.270 
[1] "0.2 - 23.9 (8.2)"  "1.6 - 91.7 (14.3)"
[1] "hr=" "1.6"
D15V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 15(12P13.31) MUTATED         0        0        1        2         3
  DEL PEAK 15(12P13.31) WILD-TYPE       3        1        0        9        16
                                 vv
clus                              STAGE IV
  DEL PEAK 15(12P13.31) MUTATED          0
  DEL PEAK 15(12P13.31) WILD-TYPE        4
D15V3, multiclass
           clus
vv          DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE
  STAGE I                               0                               3
  STAGE IA                              0                               1
  STAGE IB                              1                               0
  STAGE II                              2                               9
  STAGE III                             3                              16
  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                              T1 T2 T3+T4
  DEL PEAK 15(12P13.31) MUTATED    1  2     3
  DEL PEAK 15(12P13.31) WILD-TYPE  6 15    12
D15V4, multiclass
       clus
vv      DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE
  T1                                1                               6
  T2                                2                              15
  T3+T4                             3                              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"
                                 vv
clus                              N0 N1 N2
  DEL PEAK 15(12P13.31) MUTATED    3  1  1
  DEL PEAK 15(12P13.31) WILD-TYPE 22  5  4
D15V5, multiclass
    clus
vv   DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE
  N0                             3                              22
  N1                             1                               5
  N2                             1                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1 MX
  DEL PEAK 15(12P13.31) MUTATED    5  0  1
  DEL PEAK 15(12P13.31) WILD-TYPE 26  2  5
D15V6, multiclass
    clus
vv   DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE
  M0                             5                              26
  M1                             0                               2
  MX                             1                               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                                 cls
clus                               0  1
  DEL PEAK 15(12P13.31) MUTATED    1  5
  DEL PEAK 15(12P13.31) WILD-TYPE  9 24
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(12P13.31) MUTATED      1    5
  DEL PEAK 15(12P13.31) WILD-TYPE    9   24
        clus
vv       DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE
  FEMALE                             1                               9
  MALE                               5                              24
[1] 2 2
[1] FALSE

Clustering(16) Variable = DEL PEAK 16(13Q14.11) MUTATION ANALYSIS
D16V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 16(13Q14.11) MUTATED    5 18
  DEL PEAK 16(13Q14.11) WILD-TYPE  5 11
  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE 
                             23                              16 
  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE 
                             18                              11 
$`DEL PEAK 16(13Q14.11) MUTATED`
TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       17.95         6.08         1.87        12.20        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BS 
       18.81        23.31         5.19         3.52        10.95        13.61 
TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ 
        6.58        23.90        15.09         7.99         8.42         6.48 
TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-YS-AA4M 
       13.35        23.77        14.27         2.50         2.76 

$`DEL PEAK 16(13Q14.11) WILD-TYPE`
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LP 
        5.52         8.02        31.20         1.61         3.55        17.33 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-UD-AAC4 
       24.89        43.27        51.78         0.23        28.96        23.64 
TCGA-UD-AAC6 TCGA-UT-A88D TCGA-UT-A97Y TCGA-XT-AASU 
       14.99        21.44         4.73         4.67 

  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE 
                           1.87                            0.23 
  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE 
                          91.73                           51.78 
  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE 
                          12.20                           16.16 
[1] "1.9 - 91.7 (12.2)" "0.2 - 51.8 (16.2)"
[1] "hr=" "1.3"
D16V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 16(13Q14.11) MUTATED         2        1        0        7        10
  DEL PEAK 16(13Q14.11) WILD-TYPE       1        0        1        4         9
                                 vv
clus                              STAGE IV
  DEL PEAK 16(13Q14.11) MUTATED          3
  DEL PEAK 16(13Q14.11) WILD-TYPE        1
D16V3, multiclass
           clus
vv          DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE
  STAGE I                               2                               1
  STAGE IA                              1                               0
  STAGE IB                              0                               1
  STAGE II                              7                               4
  STAGE III                            10                               9
  STAGE IV                              3                               1
[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                              T1 T2 T3+T4
  DEL PEAK 16(13Q14.11) MUTATED    4 10     9
  DEL PEAK 16(13Q14.11) WILD-TYPE  3  7     6
D16V4, multiclass
       clus
vv      DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE
  T1                                4                               3
  T2                               10                               7
  T3+T4                             9                               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"
                                 vv
clus                              N0 N1 N2
  DEL PEAK 16(13Q14.11) MUTATED   18  1  4
  DEL PEAK 16(13Q14.11) WILD-TYPE  7  5  1
D16V5, multiclass
    clus
vv   DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE
  N0                            18                               7
  N1                             1                               5
  N2                             4                               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1 MX
  DEL PEAK 16(13Q14.11) MUTATED   20  2  1
  DEL PEAK 16(13Q14.11) WILD-TYPE 11  0  5
D16V6, multiclass
    clus
vv   DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE
  M0                            20                              11
  M1                             2                               0
  MX                             1                               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                                 cls
clus                               0  1
  DEL PEAK 16(13Q14.11) MUTATED    4 19
  DEL PEAK 16(13Q14.11) WILD-TYPE  6 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(13Q14.11) MUTATED      4   19
  DEL PEAK 16(13Q14.11) WILD-TYPE    6   10
        clus
vv       DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE
  FEMALE                             4                               6
  MALE                              19                              10
[1] 2 2
[1] FALSE

Clustering(17) Variable = DEL PEAK 17(14Q32.31) MUTATION ANALYSIS
D17V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 17(14Q32.31) MUTATED    7 12
  DEL PEAK 17(14Q32.31) WILD-TYPE  3 17
  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE 
                             19                              20 
  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE 
                             12                              17 
$`DEL PEAK 17(14Q32.31) MUTATED`
TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 
        5.52         6.08         1.87        12.20         1.61         3.55 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SH-A7BC 
       18.81        23.31        43.27        13.61         6.58        23.90 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC7 TCGA-UT-A88E TCGA-UT-A88G 
        7.99         8.42         6.48        13.35        14.27         2.50 
TCGA-UT-A97Y 
        4.73 

$`DEL PEAK 17(14Q32.31) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LM 
       17.95         8.02        31.20        80.84        91.73         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BR TCGA-NQ-A57I 
       17.33         3.52        10.95        24.89        51.78         0.23 
TCGA-SC-A6LM TCGA-SH-A7BD TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D 
       28.96        15.09        23.64        14.99        23.77        21.44 
TCGA-XT-AASU TCGA-YS-AA4M 
        4.67         2.76 

  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE 
                           1.61                            0.23 
  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE 
                          43.27                           91.73 
  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE 
                           7.99                           17.64 
[1] "1.6 - 43.3 (8.0)"  "0.2 - 91.7 (17.6)"
[1] "hr=" "1.5"
D17V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 17(14Q32.31) MUTATED         2        1        0        6        10
  DEL PEAK 17(14Q32.31) WILD-TYPE       1        0        1        5         9
                                 vv
clus                              STAGE IV
  DEL PEAK 17(14Q32.31) MUTATED          0
  DEL PEAK 17(14Q32.31) WILD-TYPE        4
D17V3, multiclass
           clus
vv          DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE
  STAGE I                               2                               1
  STAGE IA                              1                               0
  STAGE IB                              0                               1
  STAGE II                              6                               5
  STAGE III                            10                               9
  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                              T1 T2 T3+T4
  DEL PEAK 17(14Q32.31) MUTATED    3  8     8
  DEL PEAK 17(14Q32.31) WILD-TYPE  4  9     7
D17V4, multiclass
       clus
vv      DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE
  T1                                3                               4
  T2                                8                               9
  T3+T4                             8                               7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2
  DEL PEAK 17(14Q32.31) MUTATED   14  3  2
  DEL PEAK 17(14Q32.31) WILD-TYPE 11  3  3
D17V5, multiclass
    clus
vv   DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE
  N0                            14                              11
  N1                             3                               3
  N2                             2                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1 MX
  DEL PEAK 17(14Q32.31) MUTATED   17  0  2
  DEL PEAK 17(14Q32.31) WILD-TYPE 14  2  4
D17V6, multiclass
    clus
vv   DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE
  M0                            17                              14
  M1                             0                               2
  MX                             2                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                                 cls
clus                               0  1
  DEL PEAK 17(14Q32.31) MUTATED    7 12
  DEL PEAK 17(14Q32.31) WILD-TYPE  3 17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(14Q32.31) MUTATED      7   12
  DEL PEAK 17(14Q32.31) WILD-TYPE    3   17
        clus
vv       DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE
  FEMALE                             7                               3
  MALE                              12                              17
[1] 2 2
[1] FALSE

Clustering(18) Variable = DEL PEAK 18(15Q15.1) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(15Q15.1) MUTATED    3 11
  DEL PEAK 18(15Q15.1) WILD-TYPE  7 18
  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE 
                            14                             25 
  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE 
                            11                             18 
$`DEL PEAK 18(15Q15.1) MUTATED`
TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN 
        5.52         6.08        23.31        17.33         3.52        24.89 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CT 
       13.61         0.23         6.58        23.90         7.99         8.42 
TCGA-UD-AABZ TCGA-XT-AASU 
        6.48         4.67 

$`DEL PEAK 18(15Q15.1) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 
       17.95         8.02         1.87        31.20        12.20         1.61 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A6BL 
        3.55        80.84        91.73        18.81         5.19        10.95 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SH-A7BD TCGA-UD-AAC4 TCGA-UD-AAC6 
       43.27        51.78        28.96        15.09        23.64        14.99 
TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
       13.35        23.77        21.44        14.27         2.50         4.73 
TCGA-YS-AA4M 
        2.76 

  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE 
                          0.23                           1.61 
  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE 
                         24.89                          91.73 
  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE 
                         7.285                         14.990 
[1] "0.2 - 24.9 (7.3)"  "1.6 - 91.7 (15.0)"
[1] "hr=" "1.9"
D18V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 18(15Q15.1) MUTATED         0        1        1        3         9
  DEL PEAK 18(15Q15.1) WILD-TYPE       3        0        0        8        10
                                vv
clus                             STAGE IV
  DEL PEAK 18(15Q15.1) MUTATED          0
  DEL PEAK 18(15Q15.1) WILD-TYPE        4
D18V3, multiclass
           clus
vv          DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE
  STAGE I                              0                              3
  STAGE IA                             1                              0
  STAGE IB                             1                              0
  STAGE II                             3                              8
  STAGE III                            9                             10
  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                             T1 T2 T3+T4
  DEL PEAK 18(15Q15.1) MUTATED    2  6     6
  DEL PEAK 18(15Q15.1) WILD-TYPE  5 11     9
D18V4, multiclass
       clus
vv      DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE
  T1                               2                              5
  T2                               6                             11
  T3+T4                            6                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 18(15Q15.1) MUTATED    8  2  2
  DEL PEAK 18(15Q15.1) WILD-TYPE 17  4  3
D18V5, multiclass
    clus
vv   DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE
  N0                            8                             17
  N1                            2                              4
  N2                            2                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK 18(15Q15.1) MUTATED   10  0  4
  DEL PEAK 18(15Q15.1) WILD-TYPE 21  2  2
D18V6, multiclass
    clus
vv   DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE
  M0                           10                             21
  M1                            0                              2
  MX                            4                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                                cls
clus                              0  1
  DEL PEAK 18(15Q15.1) MUTATED    3 11
  DEL PEAK 18(15Q15.1) WILD-TYPE  7 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(15Q15.1) MUTATED      3   11
  DEL PEAK 18(15Q15.1) WILD-TYPE    7   18
        clus
vv       DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE
  FEMALE                            3                              7
  MALE                             11                             18
[1] 2 2
[1] FALSE

Clustering(19) Variable = DEL PEAK 19(16P13.3) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 19(16P13.3) MUTATED    1  4
  DEL PEAK 19(16P13.3) WILD-TYPE  9 25
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                             5                             34 
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                             4                             25 
$`DEL PEAK 19(16P13.3) MUTATED`
TCGA-LK-A4O0 TCGA-MQ-A4LM TCGA-MQ-A6BR TCGA-UT-A88G TCGA-UT-A97Y 
        6.08         5.19        51.78         2.50         4.73 

$`DEL PEAK 19(16P13.3) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         5.52         8.02         1.87        31.20        12.20 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.61         3.55        80.84        91.73        18.81        23.31 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS 
       17.33         3.52        10.95        24.89        43.27        13.61 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
        0.23        28.96         6.58        23.90        15.09         7.99 
TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
        8.42         6.48        23.64        14.99        13.35        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-XT-AASU TCGA-YS-AA4M 
       21.44        14.27         4.67         2.76 

  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                          2.50                           0.23 
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                         51.78                          91.73 
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                          5.19                          13.94 
[1] "2.5 - 51.8 (5.2)"  "0.2 - 91.7 (13.9)"
[1] "hr=" "1.7"
D19V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 19(16P13.3) MUTATED         1        1        0        0         3
  DEL PEAK 19(16P13.3) WILD-TYPE       2        0        1       11        16
                                vv
clus                             STAGE IV
  DEL PEAK 19(16P13.3) MUTATED          0
  DEL PEAK 19(16P13.3) WILD-TYPE        4
D19V3, multiclass
           clus
vv          DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  STAGE I                              1                              2
  STAGE IA                             1                              0
  STAGE IB                             0                              1
  STAGE II                             0                             11
  STAGE III                            3                             16
  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                             T1 T2 T3+T4
  DEL PEAK 19(16P13.3) MUTATED    3  0     2
  DEL PEAK 19(16P13.3) WILD-TYPE  4 17    13
D19V4, multiclass
       clus
vv      DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  T1                               3                              4
  T2                               0                             17
  T3+T4                            2                             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"
                                vv
clus                             N0 N1 N2
  DEL PEAK 19(16P13.3) MUTATED    4  1  0
  DEL PEAK 19(16P13.3) WILD-TYPE 21  5  5
D19V5, multiclass
    clus
vv   DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  N0                            4                             21
  N1                            1                              5
  N2                            0                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK 19(16P13.3) MUTATED    4  0  1
  DEL PEAK 19(16P13.3) WILD-TYPE 27  2  5
D19V6, multiclass
    clus
vv   DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  M0                            4                             27
  M1                            0                              2
  MX                            1                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                                cls
clus                              0  1
  DEL PEAK 19(16P13.3) MUTATED    2  3
  DEL PEAK 19(16P13.3) WILD-TYPE  8 26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(16P13.3) MUTATED      2    3
  DEL PEAK 19(16P13.3) WILD-TYPE    8   26
        clus
vv       DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  FEMALE                            2                              8
  MALE                              3                             26
[1] 2 2
[1] FALSE

Clustering(20) Variable = DEL PEAK 20(16Q24.1) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 20(16Q24.1) MUTATED    2 11
  DEL PEAK 20(16Q24.1) WILD-TYPE  8 18
  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE 
                            13                             26 
  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE 
                            11                             18 
$`DEL PEAK 20(16Q24.1) MUTATED`
TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-LK-A4O6 TCGA-MQ-A4LI TCGA-MQ-A4LJ 
       17.95         5.52         6.08         1.61        18.81        23.31 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-UD-AABZ TCGA-UD-AAC7 TCGA-UT-A88G 
       17.33         3.52        13.61         6.48        13.35         2.50 
TCGA-UT-A97Y 
        4.73 

$`DEL PEAK 20(16Q24.1) WILD-TYPE`
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O7 TCGA-MQ-A4KX 
        8.02         1.87        31.20        12.20         3.55        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       91.73         5.19        10.95        24.89        43.27        51.78 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
        0.23        28.96         6.58        23.90        15.09         7.99 
TCGA-SH-A9CT TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E 
        8.42        23.64        14.99        23.77        21.44        14.27 
TCGA-XT-AASU TCGA-YS-AA4M 
        4.67         2.76 

  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE 
                          1.61                           0.23 
  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE 
                         23.31                          91.73 
  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE 
                          6.48                          14.63 
[1] "1.6 - 23.3 (6.5)"  "0.2 - 91.7 (14.6)"
[1] "hr=" "2.8"
D20V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 20(16Q24.1) MUTATED         1        1        0        4         6
  DEL PEAK 20(16Q24.1) WILD-TYPE       2        0        1        7        13
                                vv
clus                             STAGE IV
  DEL PEAK 20(16Q24.1) MUTATED          1
  DEL PEAK 20(16Q24.1) WILD-TYPE        3
D20V3, multiclass
           clus
vv          DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE
  STAGE I                              1                              2
  STAGE IA                             1                              0
  STAGE IB                             0                              1
  STAGE II                             4                              7
  STAGE III                            6                             13
  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                             T1 T2 T3+T4
  DEL PEAK 20(16Q24.1) MUTATED    2  5     6
  DEL PEAK 20(16Q24.1) WILD-TYPE  5 12     9
D20V4, multiclass
       clus
vv      DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE
  T1                               2                              5
  T2                               5                             12
  T3+T4                            6                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 20(16Q24.1) MUTATED   10  2  1
  DEL PEAK 20(16Q24.1) WILD-TYPE 15  4  4
D20V5, multiclass
    clus
vv   DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE
  N0                           10                             15
  N1                            2                              4
  N2                            1                              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK 20(16Q24.1) MUTATED   12  0  1
  DEL PEAK 20(16Q24.1) WILD-TYPE 19  2  5
D20V6, multiclass
    clus
vv   DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE
  M0                           12                             19
  M1                            0                              2
  MX                            1                              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                                cls
clus                              0  1
  DEL PEAK 20(16Q24.1) MUTATED    4  9
  DEL PEAK 20(16Q24.1) WILD-TYPE  6 20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(16Q24.1) MUTATED      4    9
  DEL PEAK 20(16Q24.1) WILD-TYPE    6   20
        clus
vv       DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE
  FEMALE                            4                              6
  MALE                              9                             20
[1] 2 2
[1] FALSE

Clustering(21) Variable = DEL PEAK 21(22Q12.2) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 21(22Q12.2) MUTATED    9 23
  DEL PEAK 21(22Q12.2) WILD-TYPE  1  6
  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE 
                            32                              7 
  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE 
                            23                              6 
$`DEL PEAK 21(22Q12.2) MUTATED`
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
        5.52         8.02         6.08         1.87        12.20         1.61 
TCGA-LK-A4O7 TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
        3.55        91.73        18.81        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM 
        3.52        24.89        43.27        13.61         0.23        28.96 
TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-UD-AABZ TCGA-UD-AAC4 
        6.58        23.90        15.09         8.42         6.48        23.64 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G 
       14.99        13.35        23.77        21.44        14.27         2.50 
TCGA-UT-A97Y TCGA-XT-AASU 
        4.73         4.67 

$`DEL PEAK 21(22Q12.2) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A6BL TCGA-MQ-A6BR TCGA-SH-A7BH 
       17.95        31.20        80.84        10.95        51.78         7.99 
TCGA-YS-AA4M 
        2.76 

  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE 
                          0.23                           2.76 
  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE 
                         91.73                          80.84 
  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE 
                        12.775                         17.950 
[1] "0.2 - 91.7 (12.8)" "2.8 - 80.8 (17.9)"
[1] "hr=" "1.4"
D21V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 21(22Q12.2) MUTATED         2        1        1       10        16
  DEL PEAK 21(22Q12.2) WILD-TYPE       1        0        0        1         3
                                vv
clus                             STAGE IV
  DEL PEAK 21(22Q12.2) MUTATED          2
  DEL PEAK 21(22Q12.2) WILD-TYPE        2
D21V3, multiclass
           clus
vv          DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE
  STAGE I                              2                              1
  STAGE IA                             1                              0
  STAGE IB                             1                              0
  STAGE II                            10                              1
  STAGE III                           16                              3
  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                             T1 T2 T3+T4
  DEL PEAK 21(22Q12.2) MUTATED    4 15    13
  DEL PEAK 21(22Q12.2) WILD-TYPE  3  2     2
D21V4, multiclass
       clus
vv      DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE
  T1                               4                              3
  T2                              15                              2
  T3+T4                           13                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 21(22Q12.2) MUTATED   21  4  4
  DEL PEAK 21(22Q12.2) WILD-TYPE  4  2  1
D21V5, multiclass
    clus
vv   DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE
  N0                           21                              4
  N1                            4                              2
  N2                            4                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK 21(22Q12.2) MUTATED   26  1  5
  DEL PEAK 21(22Q12.2) WILD-TYPE  5  1  1
D21V6, multiclass
    clus
vv   DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE
  M0                           26                              5
  M1                            1                              1
  MX                            5                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                                cls
clus                              0  1
  DEL PEAK 21(22Q12.2) MUTATED    8 24
  DEL PEAK 21(22Q12.2) WILD-TYPE  2  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(22Q12.2) MUTATED      8   24
  DEL PEAK 21(22Q12.2) WILD-TYPE    2    5
        clus
vv       DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE
  FEMALE                            8                              2
  MALE                             24                              5
[1] 2 2
[1] FALSE
