[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/10006044/MESO-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/MESO-TP/10013766/transformed.cor.cli.txt"

nPatients in clinical file=21, in cluster file=37, common to both=21
[1] "Reduce the number of clustering variables from 23 to 21."
[1] 21 21
[1] "AMP PEAK 1(12P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(12P11.21) MUTATED AMP PEAK 1(12P11.21) WILD-TYPE 
                             7                             14 
  AMP PEAK 1(12P11.21) MUTATED AMP PEAK 1(12P11.21) WILD-TYPE 
                             7                             14 
[1] "AMP PEAK 2(17Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(17Q24.3) MUTATED AMP PEAK 2(17Q24.3) WILD-TYPE 
                            7                            14 
  AMP PEAK 2(17Q24.3) MUTATED AMP PEAK 2(17Q24.3) WILD-TYPE 
                            7                            14 
[1] "AMP PEAK 4(20P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 4(20P12.1) MUTATED AMP PEAK 4(20P12.1) WILD-TYPE 
                            3                            18 
  AMP PEAK 4(20P12.1) MUTATED AMP PEAK 4(20P12.1) WILD-TYPE 
                            3                            18 
[1] "DEL PEAK  1(1P36.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                             8                             13 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                             8                             13 
[1] "DEL PEAK  2(1P22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                            8                            13 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                            8                            13 
[1] "DEL PEAK  3(2Q35) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                          4                          17 
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                          4                          17 
[1] "DEL PEAK  4(3P21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                           15                             6 
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                           15                             6 
[1] "DEL PEAK  5(4Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                         11                          10 
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                         11                          10 
[1] "DEL PEAK  6(5Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(5Q23.2) MUTATED DEL PEAK  6(5Q23.2) WILD-TYPE 
                            3                            18 
  DEL PEAK  6(5Q23.2) MUTATED DEL PEAK  6(5Q23.2) WILD-TYPE 
                            3                            18 
[1] "DEL PEAK  7(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE 
                            13                              8 
  DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE 
                            13                              8 
[1] "DEL PEAK  8(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE 
                           12                             9 
  DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE 
                           12                             9 
[1] "DEL PEAK  9(10P15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(10P15.1) MUTATED DEL PEAK  9(10P15.1) WILD-TYPE 
                             7                             14 
  DEL PEAK  9(10P15.1) MUTATED DEL PEAK  9(10P15.1) WILD-TYPE 
                             7                             14 
[1] "DEL PEAK 10(10Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(10Q22.3) MUTATED DEL PEAK 10(10Q22.3) WILD-TYPE 
                             4                             17 
  DEL PEAK 10(10Q22.3) MUTATED DEL PEAK 10(10Q22.3) WILD-TYPE 
                             4                             17 
[1] "DEL PEAK 11(10Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(10Q24.1) MUTATED DEL PEAK 11(10Q24.1) WILD-TYPE 
                             6                             15 
  DEL PEAK 11(10Q24.1) MUTATED DEL PEAK 11(10Q24.1) WILD-TYPE 
                             6                             15 
[1] "DEL PEAK 12(13Q13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(13Q13.3) MUTATED DEL PEAK 12(13Q13.3) WILD-TYPE 
                            15                              6 
  DEL PEAK 12(13Q13.3) MUTATED DEL PEAK 12(13Q13.3) WILD-TYPE 
                            15                              6 
[1] "DEL PEAK 13(14Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(14Q11.2) MUTATED DEL PEAK 13(14Q11.2) WILD-TYPE 
                             7                             14 
  DEL PEAK 13(14Q11.2) MUTATED DEL PEAK 13(14Q11.2) WILD-TYPE 
                             7                             14 
[1] "DEL PEAK 14(14Q32.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(14Q32.31) MUTATED DEL PEAK 14(14Q32.31) WILD-TYPE 
                              8                              13 
  DEL PEAK 14(14Q32.31) MUTATED DEL PEAK 14(14Q32.31) WILD-TYPE 
                              8                              13 
[1] "DEL PEAK 15(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(15Q15.1) MUTATED DEL PEAK 15(15Q15.1) WILD-TYPE 
                             8                             13 
  DEL PEAK 15(15Q15.1) MUTATED DEL PEAK 15(15Q15.1) WILD-TYPE 
                             8                             13 
[1] "DEL PEAK 17(16Q21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE 
                           6                           15 
  DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE 
                           6                           15 
[1] "DEL PEAK 18(16Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(16Q24.1) MUTATED DEL PEAK 18(16Q24.1) WILD-TYPE 
                             6                             15 
  DEL PEAK 18(16Q24.1) MUTATED DEL PEAK 18(16Q24.1) WILD-TYPE 
                             6                             15 
[1] "DEL PEAK 19(22Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(22Q12.2) MUTATED DEL PEAK 19(22Q12.2) WILD-TYPE 
                            15                              6 
  DEL PEAK 19(22Q12.2) MUTATED DEL PEAK 19(22Q12.2) WILD-TYPE 
                            15                              6 
[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 21 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
          NA           NA           NA           NA          371           NA 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
          NA           NA           NA           NA           NA           NA 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I 
          NA           NA         1316         1575          414            7 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
          NA           NA           NA 
Variable 1:'AGE':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=5,	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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RACE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=1,	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 21 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=16, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=5, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 3 10  7  1 
[1] "table(vv)"
vv
T1+T2 T3+T4 
   13     8 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 3 10  7  1 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 13

$Class1_nSamples
[1] 8

$Class0_label
[1] "T1+T2"

$Class1_label
[1] "T3+T4"


T1+T2 T3+T4 
   13     8 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
14  4  2 
[1] "table(vv)"
vv
   N0 N1+N2 
   14     6 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
14  4  2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 14

$Class1_nSamples
[1] 6

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2"


   N0 N1+N2 
   14     6 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK 1(12P11.21) MUTATION ANALYSIS
D1V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 1(12P11.21) MUTATED    3  4
  AMP PEAK 1(12P11.21) WILD-TYPE  2 12
  AMP PEAK 1(12P11.21) MUTATED AMP PEAK 1(12P11.21) WILD-TYPE 
                             7                             14 
  AMP PEAK 1(12P11.21) MUTATED AMP PEAK 1(12P11.21) WILD-TYPE 
                             4                             12 
$`AMP PEAK 1(12P11.21) MUTATED`
TCGA-LK-A4NW TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A6BS TCGA-NQ-A57I 
       17.95         1.87        12.20        80.84        13.61         0.23 
TCGA-SH-A7BC 
       23.90 

$`AMP PEAK 1(12P11.21) WILD-TYPE`
TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
        8.02        31.20        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       17.33         3.52        10.95        24.89        43.27        51.78 
TCGA-SH-A7BD TCGA-SH-A7BH 
       15.09         7.99 

  AMP PEAK 1(12P11.21) MUTATED AMP PEAK 1(12P11.21) WILD-TYPE 
                          0.23                           3.52 
  AMP PEAK 1(12P11.21) MUTATED AMP PEAK 1(12P11.21) WILD-TYPE 
                         80.84                          91.73 
  AMP PEAK 1(12P11.21) MUTATED AMP PEAK 1(12P11.21) WILD-TYPE 
                         13.61                          18.07 
[1] "0.2 - 80.8 (13.6)" "3.5 - 91.7 (18.1)"
[1] "hr=" "1.1"
D1V2, continuous
                                vv
clus                             STAGE I STAGE IB STAGE II STAGE III STAGE IV
  AMP PEAK 1(12P11.21) MUTATED         1        1        1         3        1
  AMP PEAK 1(12P11.21) WILD-TYPE       0        0        5         8        1
D1V3, multiclass
           clus
vv          AMP PEAK 1(12P11.21) MUTATED AMP PEAK 1(12P11.21) WILD-TYPE
  STAGE I                              1                              0
  STAGE IB                             1                              0
  STAGE II                             1                              5
  STAGE III                            3                              8
  STAGE IV                             1                              1
[1] 5 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
  AMP PEAK 1(12P11.21) MUTATED       3     4
  AMP PEAK 1(12P11.21) WILD-TYPE    10     4
D1V4, multiclass
       clus
vv      AMP PEAK 1(12P11.21) MUTATED AMP PEAK 1(12P11.21) WILD-TYPE
  T1+T2                            3                             10
  T3+T4                            4                              4
[1] 2 2
[1] FALSE
                                vv
clus                             N0 N1+N2
  AMP PEAK 1(12P11.21) MUTATED    4     2
  AMP PEAK 1(12P11.21) WILD-TYPE 10     4
D1V5, multiclass
       clus
vv      AMP PEAK 1(12P11.21) MUTATED AMP PEAK 1(12P11.21) WILD-TYPE
  N0                               4                             10
  N1+N2                            2                              4
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 1(12P11.21) MUTATED    5  0  2
  AMP PEAK 1(12P11.21) WILD-TYPE 10  1  3
D1V6, multiclass
    clus
vv   AMP PEAK 1(12P11.21) MUTATED AMP PEAK 1(12P11.21) WILD-TYPE
  M0                            5                             10
  M1                            0                              1
  MX                            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"
D1V7, binary
                                cls
clus                              0  1
  AMP PEAK 1(12P11.21) MUTATED    2  5
  AMP PEAK 1(12P11.21) WILD-TYPE  4 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 1(12P11.21) MUTATED      2    5
  AMP PEAK 1(12P11.21) WILD-TYPE    4   10
        clus
vv       AMP PEAK 1(12P11.21) MUTATED AMP PEAK 1(12P11.21) WILD-TYPE
  FEMALE                            2                              4
  MALE                              5                             10
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK 2(17Q24.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 2(17Q24.3) MUTATED    3  4
  AMP PEAK 2(17Q24.3) WILD-TYPE  2 12
  AMP PEAK 2(17Q24.3) MUTATED AMP PEAK 2(17Q24.3) WILD-TYPE 
                            7                            14 
  AMP PEAK 2(17Q24.3) MUTATED AMP PEAK 2(17Q24.3) WILD-TYPE 
                            4                            12 
$`AMP PEAK 2(17Q24.3) MUTATED`
TCGA-LK-A4NW TCGA-MQ-A4LC TCGA-MQ-A4LV TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-NQ-A57I 
       17.95        91.73         3.52        43.27        13.61         0.23 
TCGA-SH-A7BC 
       23.90 

$`AMP PEAK 2(17Q24.3) WILD-TYPE`
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LI 
        8.02         1.87        31.20        12.20        80.84        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BR 
       23.31         5.19        17.33        10.95        24.89        51.78 
TCGA-SH-A7BD TCGA-SH-A7BH 
       15.09         7.99 

  AMP PEAK 2(17Q24.3) MUTATED AMP PEAK 2(17Q24.3) WILD-TYPE 
                         0.23                          1.87 
  AMP PEAK 2(17Q24.3) MUTATED AMP PEAK 2(17Q24.3) WILD-TYPE 
                        91.73                         80.84 
  AMP PEAK 2(17Q24.3) MUTATED AMP PEAK 2(17Q24.3) WILD-TYPE 
                        17.95                         16.21 
[1] "0.2 - 91.7 (17.9)" "1.9 - 80.8 (16.2)"
[1] "hr=" "2.2"
D2V2, continuous
                               vv
clus                            STAGE I STAGE IB STAGE II STAGE III STAGE IV
  AMP PEAK 2(17Q24.3) MUTATED         0        1        3         2        1
  AMP PEAK 2(17Q24.3) WILD-TYPE       1        0        3         9        1
D2V3, multiclass
           clus
vv          AMP PEAK 2(17Q24.3) MUTATED AMP PEAK 2(17Q24.3) WILD-TYPE
  STAGE I                             0                             1
  STAGE IB                            1                             0
  STAGE II                            3                             3
  STAGE III                           2                             9
  STAGE IV                            1                             1
[1] 5 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
  AMP PEAK 2(17Q24.3) MUTATED       4     3
  AMP PEAK 2(17Q24.3) WILD-TYPE     9     5
D2V4, multiclass
       clus
vv      AMP PEAK 2(17Q24.3) MUTATED AMP PEAK 2(17Q24.3) WILD-TYPE
  T1+T2                           4                             9
  T3+T4                           3                             5
[1] 2 2
[1] FALSE
                               vv
clus                            N0 N1+N2
  AMP PEAK 2(17Q24.3) MUTATED    4     2
  AMP PEAK 2(17Q24.3) WILD-TYPE 10     4
D2V5, multiclass
       clus
vv      AMP PEAK 2(17Q24.3) MUTATED AMP PEAK 2(17Q24.3) WILD-TYPE
  N0                              4                            10
  N1+N2                           2                             4
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK 2(17Q24.3) MUTATED    4  0  3
  AMP PEAK 2(17Q24.3) WILD-TYPE 11  1  2
D2V6, multiclass
    clus
vv   AMP PEAK 2(17Q24.3) MUTATED AMP PEAK 2(17Q24.3) WILD-TYPE
  M0                           4                            11
  M1                           0                             1
  MX                           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"
D2V7, binary
                               cls
clus                            0 1
  AMP PEAK 2(17Q24.3) MUTATED   0 7
  AMP PEAK 2(17Q24.3) WILD-TYPE 6 8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 2(17Q24.3) MUTATED      0    7
  AMP PEAK 2(17Q24.3) WILD-TYPE    6    8
        clus
vv       AMP PEAK 2(17Q24.3) MUTATED AMP PEAK 2(17Q24.3) WILD-TYPE
  FEMALE                           0                             6
  MALE                             7                             8
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK 4(20P12.1) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 4(20P12.1) MUTATED    1  2
  AMP PEAK 4(20P12.1) WILD-TYPE  4 14
  AMP PEAK 4(20P12.1) MUTATED AMP PEAK 4(20P12.1) WILD-TYPE 
                            3                            18 
  AMP PEAK 4(20P12.1) MUTATED AMP PEAK 4(20P12.1) WILD-TYPE 
                            2                            14 
$`AMP PEAK 4(20P12.1) MUTATED`
TCGA-MQ-A4LC TCGA-MQ-A6BL TCGA-NQ-A57I 
       91.73        10.95         0.23 

$`AMP PEAK 4(20P12.1) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN 
       18.81        23.31         5.19        17.33         3.52        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       43.27        51.78        13.61        23.90        15.09         7.99 

  AMP PEAK 4(20P12.1) MUTATED AMP PEAK 4(20P12.1) WILD-TYPE 
                         0.23                          1.87 
  AMP PEAK 4(20P12.1) MUTATED AMP PEAK 4(20P12.1) WILD-TYPE 
                        91.73                         80.84 
  AMP PEAK 4(20P12.1) MUTATED AMP PEAK 4(20P12.1) WILD-TYPE 
                        10.95                         17.64 
[1] "0.2 - 91.7 (10.9)" "1.9 - 80.8 (17.6)"
[1] "hr=" "2.6"
D3V2, continuous
                               vv
clus                            STAGE I STAGE IB STAGE II STAGE III STAGE IV
  AMP PEAK 4(20P12.1) MUTATED         0        1        2         0        0
  AMP PEAK 4(20P12.1) WILD-TYPE       1        0        4        11        2
D3V3, multiclass
           clus
vv          AMP PEAK 4(20P12.1) MUTATED AMP PEAK 4(20P12.1) WILD-TYPE
  STAGE I                             0                             1
  STAGE IB                            1                             0
  STAGE II                            2                             4
  STAGE III                           0                            11
  STAGE IV                            0                             2
[1] 5 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
  AMP PEAK 4(20P12.1) MUTATED       3     0
  AMP PEAK 4(20P12.1) WILD-TYPE    10     8
D3V4, multiclass
       clus
vv      AMP PEAK 4(20P12.1) MUTATED AMP PEAK 4(20P12.1) WILD-TYPE
  T1+T2                           3                            10
  T3+T4                           0                             8
[1] 2 2
[1] FALSE
                               vv
clus                            N0 N1+N2
  AMP PEAK 4(20P12.1) MUTATED    2     0
  AMP PEAK 4(20P12.1) WILD-TYPE 12     6
D3V5, multiclass
[1] "Remove cluster labels:"      "AMP PEAK 4(20P12.1) MUTATED"
clus
  AMP PEAK 4(20P12.1) MUTATED AMP PEAK 4(20P12.1) WILD-TYPE 
                            2                            18 
                   TCGA-LK-A4NW                    TCGA-LK-A4NZ 
"AMP PEAK 4(20P12.1) WILD-TYPE" "AMP PEAK 4(20P12.1) WILD-TYPE" 
                   TCGA-LK-A4O2                    TCGA-LK-A4O4 
"AMP PEAK 4(20P12.1) WILD-TYPE" "AMP PEAK 4(20P12.1) WILD-TYPE" 
                   TCGA-LK-A4O5                    TCGA-MQ-A4KX 
"AMP PEAK 4(20P12.1) WILD-TYPE" "AMP PEAK 4(20P12.1) WILD-TYPE" 
                   TCGA-MQ-A4LI                    TCGA-MQ-A4LJ 
"AMP PEAK 4(20P12.1) WILD-TYPE" "AMP PEAK 4(20P12.1) WILD-TYPE" 
                   TCGA-MQ-A4LM                    TCGA-MQ-A4LP 
"AMP PEAK 4(20P12.1) WILD-TYPE" "AMP PEAK 4(20P12.1) WILD-TYPE" 
                   TCGA-MQ-A4LV                    TCGA-MQ-A6BN 
"AMP PEAK 4(20P12.1) WILD-TYPE" "AMP PEAK 4(20P12.1) WILD-TYPE" 
                   TCGA-MQ-A6BQ                    TCGA-MQ-A6BR 
"AMP PEAK 4(20P12.1) WILD-TYPE" "AMP PEAK 4(20P12.1) WILD-TYPE" 
                   TCGA-MQ-A6BS                    TCGA-SH-A7BC 
"AMP PEAK 4(20P12.1) WILD-TYPE" "AMP PEAK 4(20P12.1) WILD-TYPE" 
                   TCGA-SH-A7BD                    TCGA-SH-A7BH 
"AMP PEAK 4(20P12.1) WILD-TYPE" "AMP PEAK 4(20P12.1) WILD-TYPE" 
                               vv
clus                            M0 M1 MX
  AMP PEAK 4(20P12.1) MUTATED    2  0  1
  AMP PEAK 4(20P12.1) WILD-TYPE 13  1  4
D3V6, multiclass
    clus
vv   AMP PEAK 4(20P12.1) MUTATED AMP PEAK 4(20P12.1) WILD-TYPE
  M0                           2                            13
  M1                           0                             1
  MX                           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"
D3V7, binary
                               cls
clus                             0  1
  AMP PEAK 4(20P12.1) MUTATED    0  3
  AMP PEAK 4(20P12.1) WILD-TYPE  6 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(20P12.1) MUTATED      0    3
  AMP PEAK 4(20P12.1) WILD-TYPE    6   12
        clus
vv       AMP PEAK 4(20P12.1) MUTATED AMP PEAK 4(20P12.1) WILD-TYPE
  FEMALE                           0                             6
  MALE                             3                            12
[1] 2 2
[1] FALSE

Clustering(4) Variable = DEL PEAK  1(1P36.23) MUTATION ANALYSIS
D4V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.23) MUTATED    2  6
  DEL PEAK  1(1P36.23) WILD-TYPE  3 10
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                             8                             13 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                             6                             10 
$`DEL PEAK  1(1P36.23) MUTATED`
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A6BL 
        8.02         1.87        12.20        18.81         5.19        10.95 
TCGA-MQ-A6BS TCGA-SH-A7BC 
       13.61        23.90 

$`DEL PEAK  1(1P36.23) 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-SH-A7BD 
        3.52        24.89        43.27        51.78         0.23        15.09 
TCGA-SH-A7BH 
        7.99 

  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                          1.87                           0.23 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                         23.90                          91.73 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                        11.575                         23.310 
[1] "1.9 - 23.9 (11.6)" "0.2 - 91.7 (23.3)"
[1] "hr=" "2.9"
D4V2, continuous
                                vv
clus                             STAGE I STAGE IB STAGE II STAGE III STAGE IV
  DEL PEAK  1(1P36.23) MUTATED         0        0        4         4        0
  DEL PEAK  1(1P36.23) WILD-TYPE       1        1        2         7        2
D4V3, multiclass
           clus
vv          DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  STAGE I                              0                              1
  STAGE IB                             0                              1
  STAGE II                             4                              2
  STAGE III                            4                              7
  STAGE IV                             0                              2
[1] 5 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(1P36.23) MUTATED       4     4
  DEL PEAK  1(1P36.23) WILD-TYPE     9     4
D4V4, multiclass
       clus
vv      DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  T1+T2                            4                              9
  T3+T4                            4                              4
[1] 2 2
[1] FALSE
                                vv
clus                             N0 N1+N2
  DEL PEAK  1(1P36.23) MUTATED    7     1
  DEL PEAK  1(1P36.23) WILD-TYPE  7     5
D4V5, multiclass
       clus
vv      DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  N0                               7                              7
  N1+N2                            1                              5
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK  1(1P36.23) MUTATED    7  0  1
  DEL PEAK  1(1P36.23) WILD-TYPE  8  1  4
D4V6, multiclass
    clus
vv   DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  M0                            7                              8
  M1                            0                              1
  MX                            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"
D4V7, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED    3  5
  DEL PEAK  1(1P36.23) WILD-TYPE  3 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      3    5
  DEL PEAK  1(1P36.23) WILD-TYPE    3   10
        clus
vv       DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  FEMALE                            3                              3
  MALE                              5                             10
[1] 2 2
[1] FALSE

Clustering(5) Variable = DEL PEAK  2(1P22.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                           0 1
  DEL PEAK  2(1P22.1) MUTATED   1 7
  DEL PEAK  2(1P22.1) WILD-TYPE 4 9
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                            8                            13 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                            7                             9 
$`DEL PEAK  2(1P22.1) MUTATED`
TCGA-LK-A4O2 TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A6BL 
        1.87        91.73        18.81        23.31        17.33        10.95 
TCGA-MQ-A6BS TCGA-SH-A7BD 
       13.61        15.09 

$`DEL PEAK  2(1P22.1) 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 
        7.99 

  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                         1.87                          0.23 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                        91.73                         80.84 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                        16.21                         17.95 
[1] "1.9 - 91.7 (16.2)" "0.2 - 80.8 (17.9)"
[1] "hr=" "1.3"
D5V2, continuous
                               vv
clus                            STAGE I STAGE IB STAGE II STAGE III STAGE IV
  DEL PEAK  2(1P22.1) MUTATED         0        0        4         3        1
  DEL PEAK  2(1P22.1) WILD-TYPE       1        1        2         8        1
D5V3, multiclass
           clus
vv          DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  STAGE I                             0                             1
  STAGE IB                            0                             1
  STAGE II                            4                             2
  STAGE III                           3                             8
  STAGE IV                            1                             1
[1] 5 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(1P22.1) MUTATED       6     2
  DEL PEAK  2(1P22.1) WILD-TYPE     7     6
D5V4, multiclass
       clus
vv      DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  T1+T2                           6                             7
  T3+T4                           2                             6
[1] 2 2
[1] FALSE
                               vv
clus                            N0 N1+N2
  DEL PEAK  2(1P22.1) MUTATED    7     1
  DEL PEAK  2(1P22.1) WILD-TYPE  7     5
D5V5, multiclass
       clus
vv      DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  N0                              7                             7
  N1+N2                           1                             5
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  2(1P22.1) MUTATED    6  1  1
  DEL PEAK  2(1P22.1) WILD-TYPE  9  0  4
D5V6, multiclass
    clus
vv   DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  M0                           6                             9
  M1                           1                             0
  MX                           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"
D5V7, binary
                               cls
clus                            0 1
  DEL PEAK  2(1P22.1) MUTATED   2 6
  DEL PEAK  2(1P22.1) WILD-TYPE 4 9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED      2    6
  DEL PEAK  2(1P22.1) WILD-TYPE    4    9
        clus
vv       DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  FEMALE                           2                             4
  MALE                             6                             9
[1] 2 2
[1] FALSE

Clustering(6) Variable = DEL PEAK  3(2Q35) MUTATION ANALYSIS
D6V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  3(2Q35) MUTATED    1  3
  DEL PEAK  3(2Q35) WILD-TYPE  4 13
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                          4                          17 
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                          3                          13 
$`DEL PEAK  3(2Q35) MUTATED`
TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4LI TCGA-SH-A7BH 
        1.87        12.20        18.81         7.99 

$`DEL PEAK  3(2Q35) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ 
       17.95         8.02        31.20        80.84        91.73        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-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BD 
       51.78        13.61         0.23        23.90        15.09 

  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 
                     10.095                      17.950 
[1] "1.9 - 18.8 (10.1)" "0.2 - 91.7 (17.9)"
[1] "hr=" "2.8"
D6V2, continuous
                             vv
clus                          STAGE I STAGE IB STAGE II STAGE III STAGE IV
  DEL PEAK  3(2Q35) MUTATED         0        0        1         3        0
  DEL PEAK  3(2Q35) WILD-TYPE       1        1        5         8        2
D6V3, multiclass
           clus
vv          DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  STAGE I                           0                           1
  STAGE IB                          0                           1
  STAGE II                          1                           5
  STAGE III                         3                           8
  STAGE IV                          0                           2
[1] 5 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     3
  DEL PEAK  3(2Q35) WILD-TYPE    12     5
D6V4, multiclass
       clus
vv      DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  T1+T2                         1                          12
  T3+T4                         3                           5
[1] 2 2
[1] FALSE
                             vv
clus                          N0 N1+N2
  DEL PEAK  3(2Q35) MUTATED    4     0
  DEL PEAK  3(2Q35) WILD-TYPE 10     6
D6V5, multiclass
       clus
vv      DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  N0                            4                          10
  N1+N2                         0                           6
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  DEL PEAK  3(2Q35) MUTATED    4  0  0
  DEL PEAK  3(2Q35) WILD-TYPE 11  1  5
D6V6, multiclass
    clus
vv   DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  M0                         4                          11
  M1                         0                           1
  MX                         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"
D6V7, binary
                             cls
clus                           0  1
  DEL PEAK  3(2Q35) MUTATED    4  0
  DEL PEAK  3(2Q35) WILD-TYPE  2 15
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(2Q35) MUTATED      4    0
  DEL PEAK  3(2Q35) WILD-TYPE    2   15
        clus
vv       DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  FEMALE                         4                           2
  MALE                           0                          15
[1] 2 2
[1] FALSE

Clustering(7) Variable = DEL PEAK  4(3P21.1) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(3P21.1) MUTATED    3 12
  DEL PEAK  4(3P21.1) WILD-TYPE  2  4
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                           15                             6 
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                           12                             4 
$`DEL PEAK  4(3P21.1) MUTATED`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       17.95         8.02         1.87        12.20        80.84        91.73 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BS 
        5.19        17.33         3.52        10.95        24.89        13.61 
TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BD 
        0.23        23.90        15.09 

$`DEL PEAK  4(3P21.1) WILD-TYPE`
TCGA-LK-A4O4 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SH-A7BH 
       31.20        18.81        23.31        43.27        51.78         7.99 

  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                         0.23                          7.99 
  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                        27.255 
[1] "0.2 - 91.7 (13.6)" "8.0 - 51.8 (27.3)"
[1] "hr=" "1.9"
D7V2, continuous
                               vv
clus                            STAGE I STAGE IB STAGE II STAGE III STAGE IV
  DEL PEAK  4(3P21.1) MUTATED         1        1        4         7        2
  DEL PEAK  4(3P21.1) WILD-TYPE       0        0        2         4        0
D7V3, multiclass
           clus
vv          DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  STAGE I                             1                             0
  STAGE IB                            1                             0
  STAGE II                            4                             2
  STAGE III                           7                             4
  STAGE IV                            2                             0
[1] 5 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       8     7
  DEL PEAK  4(3P21.1) WILD-TYPE     5     1
D7V4, multiclass
       clus
vv      DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  T1+T2                           8                             5
  T3+T4                           7                             1
[1] 2 2
[1] FALSE
                               vv
clus                            N0 N1+N2
  DEL PEAK  4(3P21.1) MUTATED   11     3
  DEL PEAK  4(3P21.1) WILD-TYPE  3     3
D7V5, multiclass
       clus
vv      DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  N0                             11                             3
  N1+N2                           3                             3
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  4(3P21.1) MUTATED   11  1  3
  DEL PEAK  4(3P21.1) WILD-TYPE  4  0  2
D7V6, multiclass
    clus
vv   DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  M0                          11                             4
  M1                           1                             0
  MX                           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"
D7V7, binary
                               cls
clus                             0  1
  DEL PEAK  4(3P21.1) MUTATED    3 12
  DEL PEAK  4(3P21.1) WILD-TYPE  3  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P21.1) MUTATED      3   12
  DEL PEAK  4(3P21.1) WILD-TYPE    3    3
        clus
vv       DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  FEMALE                           3                             3
  MALE                            12                             3
[1] 2 2
[1] FALSE

Clustering(8) Variable = DEL PEAK  5(4Q26) MUTATION ANALYSIS
D8V1, survival
                             sevent
clus2                         0 1
  DEL PEAK  5(4Q26) MUTATED   3 8
  DEL PEAK  5(4Q26) WILD-TYPE 2 8
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                         11                          10 
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                          8                           8 
$`DEL PEAK  5(4Q26) MUTATED`
TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
        1.87        12.20        18.81         5.19        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SH-A7BC TCGA-SH-A7BH 
       10.95        51.78        13.61        23.90         7.99 

$`DEL PEAK  5(4Q26) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ 
       17.95         8.02        31.20        80.84        91.73        23.31 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-NQ-A57I TCGA-SH-A7BD 
       24.89        43.27         0.23        15.09 

  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                       1.87                        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 
                       12.2                        24.1 
[1] "1.9 - 51.8 (12.2)" "0.2 - 91.7 (24.1)"
[1] "hr=" "2.4"
D8V2, continuous
                             vv
clus                          STAGE I STAGE IB STAGE II STAGE III STAGE IV
  DEL PEAK  5(4Q26) MUTATED         0        0        3         8        0
  DEL PEAK  5(4Q26) WILD-TYPE       1        1        3         3        2
D8V3, multiclass
           clus
vv          DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  STAGE I                           0                           1
  STAGE IB                          0                           1
  STAGE II                          3                           3
  STAGE III                         8                           3
  STAGE IV                          0                           2
[1] 5 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       4     7
  DEL PEAK  5(4Q26) WILD-TYPE     9     1
D8V4, multiclass
       clus
vv      DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  T1+T2                         4                           9
  T3+T4                         7                           1
[1] 2 2
[1] FALSE
                             vv
clus                          N0 N1+N2
  DEL PEAK  5(4Q26) MUTATED    9     2
  DEL PEAK  5(4Q26) WILD-TYPE  5     4
D8V5, multiclass
       clus
vv      DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  N0                            9                           5
  N1+N2                         2                           4
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  DEL PEAK  5(4Q26) MUTATED    9  0  2
  DEL PEAK  5(4Q26) WILD-TYPE  6  1  3
D8V6, multiclass
    clus
vv   DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  M0                         9                           6
  M1                         0                           1
  MX                         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"
D8V7, binary
                             cls
clus                          0 1
  DEL PEAK  5(4Q26) MUTATED   5 6
  DEL PEAK  5(4Q26) WILD-TYPE 1 9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(4Q26) MUTATED      5    6
  DEL PEAK  5(4Q26) WILD-TYPE    1    9
        clus
vv       DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  FEMALE                         5                           1
  MALE                           6                           9
[1] 2 2
[1] FALSE

Clustering(9) Variable = DEL PEAK  6(5Q23.2) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(5Q23.2) MUTATED    1  2
  DEL PEAK  6(5Q23.2) WILD-TYPE  4 14
  DEL PEAK  6(5Q23.2) MUTATED DEL PEAK  6(5Q23.2) WILD-TYPE 
                            3                            18 
  DEL PEAK  6(5Q23.2) MUTATED DEL PEAK  6(5Q23.2) WILD-TYPE 
                            2                            14 
$`DEL PEAK  6(5Q23.2) MUTATED`
TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-SH-A7BD 
        3.52        13.61        15.09 

$`DEL PEAK  6(5Q23.2) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A6BL 
       91.73        18.81        23.31         5.19        17.33        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BH 
       24.89        43.27        51.78         0.23        23.90         7.99 

  DEL PEAK  6(5Q23.2) MUTATED DEL PEAK  6(5Q23.2) WILD-TYPE 
                         3.52                          0.23 
  DEL PEAK  6(5Q23.2) MUTATED DEL PEAK  6(5Q23.2) WILD-TYPE 
                        15.09                         91.73 
  DEL PEAK  6(5Q23.2) MUTATED DEL PEAK  6(5Q23.2) WILD-TYPE 
                        13.61                         18.38 
[1] "3.5 - 15.1 (13.6)" "0.2 - 91.7 (18.4)"
[1] "hr=" "2.8"
D9V2, continuous
                               vv
clus                            STAGE I STAGE IB STAGE II STAGE III STAGE IV
  DEL PEAK  6(5Q23.2) MUTATED         0        0        1         1        1
  DEL PEAK  6(5Q23.2) WILD-TYPE       1        1        5        10        1
D9V3, multiclass
           clus
vv          DEL PEAK  6(5Q23.2) MUTATED DEL PEAK  6(5Q23.2) WILD-TYPE
  STAGE I                             0                             1
  STAGE IB                            0                             1
  STAGE II                            1                             5
  STAGE III                           1                            10
  STAGE IV                            1                             1
[1] 5 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(5Q23.2) MUTATED       2     1
  DEL PEAK  6(5Q23.2) WILD-TYPE    11     7
D9V4, multiclass
       clus
vv      DEL PEAK  6(5Q23.2) MUTATED DEL PEAK  6(5Q23.2) WILD-TYPE
  T1+T2                           2                            11
  T3+T4                           1                             7
[1] 2 2
[1] FALSE
                               vv
clus                            N0 N1+N2
  DEL PEAK  6(5Q23.2) MUTATED    3     0
  DEL PEAK  6(5Q23.2) WILD-TYPE 11     6
D9V5, multiclass
       clus
vv      DEL PEAK  6(5Q23.2) MUTATED DEL PEAK  6(5Q23.2) WILD-TYPE
  N0                              3                            11
  N1+N2                           0                             6
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  6(5Q23.2) MUTATED    1  1  1
  DEL PEAK  6(5Q23.2) WILD-TYPE 14  0  4
D9V6, multiclass
    clus
vv   DEL PEAK  6(5Q23.2) MUTATED DEL PEAK  6(5Q23.2) WILD-TYPE
  M0                           1                            14
  M1                           1                             0
  MX                           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"
D9V7, binary
                               cls
clus                             0  1
  DEL PEAK  6(5Q23.2) MUTATED    0  3
  DEL PEAK  6(5Q23.2) WILD-TYPE  6 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(5Q23.2) MUTATED      0    3
  DEL PEAK  6(5Q23.2) WILD-TYPE    6   12
        clus
vv       DEL PEAK  6(5Q23.2) MUTATED DEL PEAK  6(5Q23.2) WILD-TYPE
  FEMALE                           0                             6
  MALE                             3                            12
[1] 2 2
[1] FALSE

Clustering(10) Variable = DEL PEAK  7(6Q22.31) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  7(6Q22.31) MUTATED    3 10
  DEL PEAK  7(6Q22.31) WILD-TYPE  2  6
  DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE 
                            13                              8 
  DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE 
                            10                              6 
$`DEL PEAK  7(6Q22.31) MUTATED`
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LM 
        8.02         1.87        80.84        91.73        18.81         5.19 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BC 
       10.95        24.89        43.27        13.61         0.23        23.90 
TCGA-SH-A7BD 
       15.09 

$`DEL PEAK  7(6Q22.31) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV 
       17.95        31.20        12.20        23.31        17.33         3.52 
TCGA-MQ-A6BR TCGA-SH-A7BH 
       51.78         7.99 

  DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE 
                          0.23                           3.52 
  DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE 
                         91.73                          51.78 
  DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE 
                         15.09                          17.64 
[1] "0.2 - 91.7 (15.1)" "3.5 - 51.8 (17.6)"
[1] "hr=" "1.2"
D10V2, continuous
                                vv
clus                             STAGE I STAGE IB STAGE II STAGE III STAGE IV
  DEL PEAK  7(6Q22.31) MUTATED         1        1        6         4        1
  DEL PEAK  7(6Q22.31) WILD-TYPE       0        0        0         7        1
D10V3, multiclass
           clus
vv          DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE
  STAGE I                              1                              0
  STAGE IB                             1                              0
  STAGE II                             6                              0
  STAGE III                            4                              7
  STAGE IV                             1                              1
[1] 5 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(6Q22.31) MUTATED      10     3
  DEL PEAK  7(6Q22.31) WILD-TYPE     3     5
D10V4, multiclass
       clus
vv      DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE
  T1+T2                           10                              3
  T3+T4                            3                              5
[1] 2 2
[1] FALSE
                                vv
clus                             N0 N1+N2
  DEL PEAK  7(6Q22.31) MUTATED   10     2
  DEL PEAK  7(6Q22.31) WILD-TYPE  4     4
D10V5, multiclass
       clus
vv      DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE
  N0                              10                              4
  N1+N2                            2                              4
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK  7(6Q22.31) MUTATED    8  1  4
  DEL PEAK  7(6Q22.31) WILD-TYPE  7  0  1
D10V6, multiclass
    clus
vv   DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE
  M0                            8                              7
  M1                            1                              0
  MX                            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"
D10V7, binary
                                cls
clus                              0  1
  DEL PEAK  7(6Q22.31) MUTATED    3 10
  DEL PEAK  7(6Q22.31) WILD-TYPE  3  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(6Q22.31) MUTATED      3   10
  DEL PEAK  7(6Q22.31) WILD-TYPE    3    5
        clus
vv       DEL PEAK  7(6Q22.31) MUTATED DEL PEAK  7(6Q22.31) WILD-TYPE
  FEMALE                            3                              3
  MALE                             10                              5
[1] 2 2
[1] FALSE

Clustering(11) Variable = DEL PEAK  8(9P21.3) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                           0 1
  DEL PEAK  8(9P21.3) MUTATED   3 9
  DEL PEAK  8(9P21.3) WILD-TYPE 2 7
  DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE 
                           12                             9 
  DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE 
                            9                             7 
$`DEL PEAK  8(9P21.3) MUTATED`
TCGA-LK-A4NW TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       17.95         1.87        12.20        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BC 
       17.33         3.52        10.95        13.61         0.23        23.90 

$`DEL PEAK  8(9P21.3) WILD-TYPE`
TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        8.02        31.20        80.84        91.73        24.89        43.27 
TCGA-MQ-A6BR TCGA-SH-A7BD TCGA-SH-A7BH 
       51.78        15.09         7.99 

  DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE 
                         0.23                          7.99 
  DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE 
                        23.90                         91.73 
  DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE 
                       12.905                        31.200 
[1] "0.2 - 23.9 (12.9)" "8.0 - 91.7 (31.2)"
[1] "hr=" "4.6"
D11V2, continuous
                               vv
clus                            STAGE I STAGE IB STAGE II STAGE III STAGE IV
  DEL PEAK  8(9P21.3) MUTATED         0        1        3         7        1
  DEL PEAK  8(9P21.3) WILD-TYPE       1        0        3         4        1
D11V3, multiclass
           clus
vv          DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE
  STAGE I                             0                             1
  STAGE IB                            1                             0
  STAGE II                            3                             3
  STAGE III                           7                             4
  STAGE IV                            1                             1
[1] 5 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(9P21.3) MUTATED       5     7
  DEL PEAK  8(9P21.3) WILD-TYPE     8     1
D11V4, multiclass
       clus
vv      DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE
  T1+T2                           5                             8
  T3+T4                           7                             1
[1] 2 2
[1] FALSE
                               vv
clus                            N0 N1+N2
  DEL PEAK  8(9P21.3) MUTATED    8     3
  DEL PEAK  8(9P21.3) WILD-TYPE  6     3
D11V5, multiclass
       clus
vv      DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE
  N0                              8                             6
  N1+N2                           3                             3
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  8(9P21.3) MUTATED   10  0  2
  DEL PEAK  8(9P21.3) WILD-TYPE  5  1  3
D11V6, multiclass
    clus
vv   DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE
  M0                          10                             5
  M1                           0                             1
  MX                           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"
D11V7, binary
                               cls
clus                            0 1
  DEL PEAK  8(9P21.3) MUTATED   3 9
  DEL PEAK  8(9P21.3) WILD-TYPE 3 6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(9P21.3) MUTATED      3    9
  DEL PEAK  8(9P21.3) WILD-TYPE    3    6
        clus
vv       DEL PEAK  8(9P21.3) MUTATED DEL PEAK  8(9P21.3) WILD-TYPE
  FEMALE                           3                             3
  MALE                             9                             6
[1] 2 2
[1] FALSE

Clustering(12) Variable = DEL PEAK  9(10P15.1) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  9(10P15.1) MUTATED    2  5
  DEL PEAK  9(10P15.1) WILD-TYPE  3 11
  DEL PEAK  9(10P15.1) MUTATED DEL PEAK  9(10P15.1) WILD-TYPE 
                             7                             14 
  DEL PEAK  9(10P15.1) MUTATED DEL PEAK  9(10P15.1) WILD-TYPE 
                             5                             11 
$`DEL PEAK  9(10P15.1) MUTATED`
TCGA-LK-A4O2 TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-NQ-A57I 
        1.87         5.19        17.33         3.52        13.61         0.23 
TCGA-SH-A7BH 
        7.99 

$`DEL PEAK  9(10P15.1) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       17.95         8.02        31.20        12.20        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       18.81        23.31        10.95        24.89        43.27        51.78 
TCGA-SH-A7BC TCGA-SH-A7BD 
       23.90        15.09 

  DEL PEAK  9(10P15.1) MUTATED DEL PEAK  9(10P15.1) WILD-TYPE 
                          0.23                           8.02 
  DEL PEAK  9(10P15.1) MUTATED DEL PEAK  9(10P15.1) WILD-TYPE 
                         17.33                          91.73 
  DEL PEAK  9(10P15.1) MUTATED DEL PEAK  9(10P15.1) WILD-TYPE 
                         5.190                         23.605 
[1] "0.2 - 17.3 (5.2)"  "8.0 - 91.7 (23.6)"
[1] "hr=" "9"  
D12V2, continuous
                                vv
clus                             STAGE I STAGE IB STAGE II STAGE III STAGE IV
  DEL PEAK  9(10P15.1) MUTATED         0        1        1         5        0
  DEL PEAK  9(10P15.1) WILD-TYPE       1        0        5         6        2
D12V3, multiclass
           clus
vv          DEL PEAK  9(10P15.1) MUTATED DEL PEAK  9(10P15.1) WILD-TYPE
  STAGE I                              0                              1
  STAGE IB                             1                              0
  STAGE II                             1                              5
  STAGE III                            5                              6
  STAGE IV                             0                              2
[1] 5 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(10P15.1) MUTATED       2     5
  DEL PEAK  9(10P15.1) WILD-TYPE    11     3
D12V4, multiclass
       clus
vv      DEL PEAK  9(10P15.1) MUTATED DEL PEAK  9(10P15.1) WILD-TYPE
  T1+T2                            2                             11
  T3+T4                            5                              3
[1] 2 2
[1] FALSE
                                vv
clus                             N0 N1+N2
  DEL PEAK  9(10P15.1) MUTATED    6     0
  DEL PEAK  9(10P15.1) WILD-TYPE  8     6
D12V5, multiclass
       clus
vv      DEL PEAK  9(10P15.1) MUTATED DEL PEAK  9(10P15.1) WILD-TYPE
  N0                               6                              8
  N1+N2                            0                              6
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK  9(10P15.1) MUTATED    5  0  2
  DEL PEAK  9(10P15.1) WILD-TYPE 10  1  3
D12V6, multiclass
    clus
vv   DEL PEAK  9(10P15.1) MUTATED DEL PEAK  9(10P15.1) WILD-TYPE
  M0                            5                             10
  M1                            0                              1
  MX                            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"
D12V7, binary
                                cls
clus                              0  1
  DEL PEAK  9(10P15.1) MUTATED    2  5
  DEL PEAK  9(10P15.1) WILD-TYPE  4 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(10P15.1) MUTATED      2    5
  DEL PEAK  9(10P15.1) WILD-TYPE    4   10
        clus
vv       DEL PEAK  9(10P15.1) MUTATED DEL PEAK  9(10P15.1) WILD-TYPE
  FEMALE                            2                              4
  MALE                              5                             10
[1] 2 2
[1] FALSE

Clustering(13) Variable = DEL PEAK 10(10Q22.3) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 10(10Q22.3) MUTATED    2  2
  DEL PEAK 10(10Q22.3) WILD-TYPE  3 14
  DEL PEAK 10(10Q22.3) MUTATED DEL PEAK 10(10Q22.3) WILD-TYPE 
                             4                             17 
  DEL PEAK 10(10Q22.3) MUTATED DEL PEAK 10(10Q22.3) WILD-TYPE 
                             2                             14 
$`DEL PEAK 10(10Q22.3) MUTATED`
TCGA-MQ-A4LP TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BH 
       17.33        13.61         0.23         7.99 

$`DEL PEAK 10(10Q22.3) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL 
       91.73        18.81        23.31         5.19         3.52        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SH-A7BC TCGA-SH-A7BD 
       24.89        43.27        51.78        23.90        15.09 

  DEL PEAK 10(10Q22.3) MUTATED DEL PEAK 10(10Q22.3) WILD-TYPE 
                          0.23                           1.87 
  DEL PEAK 10(10Q22.3) MUTATED DEL PEAK 10(10Q22.3) WILD-TYPE 
                         17.33                          91.73 
  DEL PEAK 10(10Q22.3) MUTATED DEL PEAK 10(10Q22.3) WILD-TYPE 
                         10.80                          18.81 
[1] "0.2 - 17.3 (10.8)" "1.9 - 91.7 (18.8)"
[1] "hr=" "2.1"
D13V2, continuous
                                vv
clus                             STAGE I STAGE IB STAGE II STAGE III STAGE IV
  DEL PEAK 10(10Q22.3) MUTATED         0        1        1         2        0
  DEL PEAK 10(10Q22.3) WILD-TYPE       1        0        5         9        2
D13V3, multiclass
           clus
vv          DEL PEAK 10(10Q22.3) MUTATED DEL PEAK 10(10Q22.3) WILD-TYPE
  STAGE I                              0                              1
  STAGE IB                             1                              0
  STAGE II                             1                              5
  STAGE III                            2                              9
  STAGE IV                             0                              2
[1] 5 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(10Q22.3) MUTATED       2     2
  DEL PEAK 10(10Q22.3) WILD-TYPE    11     6
D13V4, multiclass
       clus
vv      DEL PEAK 10(10Q22.3) MUTATED DEL PEAK 10(10Q22.3) WILD-TYPE
  T1+T2                            2                             11
  T3+T4                            2                              6
[1] 2 2
[1] FALSE
                                vv
clus                             N0 N1+N2
  DEL PEAK 10(10Q22.3) MUTATED    3     0
  DEL PEAK 10(10Q22.3) WILD-TYPE 11     6
D13V5, multiclass
       clus
vv      DEL PEAK 10(10Q22.3) MUTATED DEL PEAK 10(10Q22.3) WILD-TYPE
  N0                               3                             11
  N1+N2                            0                              6
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 10(10Q22.3) MUTATED    2  0  2
  DEL PEAK 10(10Q22.3) WILD-TYPE 13  1  3
D13V6, multiclass
    clus
vv   DEL PEAK 10(10Q22.3) MUTATED DEL PEAK 10(10Q22.3) WILD-TYPE
  M0                            2                             13
  M1                            0                              1
  MX                            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"
D13V7, binary
                                cls
clus                              0  1
  DEL PEAK 10(10Q22.3) MUTATED    1  3
  DEL PEAK 10(10Q22.3) WILD-TYPE  5 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(10Q22.3) MUTATED      1    3
  DEL PEAK 10(10Q22.3) WILD-TYPE    5   12
        clus
vv       DEL PEAK 10(10Q22.3) MUTATED DEL PEAK 10(10Q22.3) WILD-TYPE
  FEMALE                            1                              5
  MALE                              3                             12
[1] 2 2
[1] FALSE

Clustering(14) Variable = DEL PEAK 11(10Q24.1) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 11(10Q24.1) MUTATED    2  4
  DEL PEAK 11(10Q24.1) WILD-TYPE  3 12
  DEL PEAK 11(10Q24.1) MUTATED DEL PEAK 11(10Q24.1) WILD-TYPE 
                             6                             15 
  DEL PEAK 11(10Q24.1) MUTATED DEL PEAK 11(10Q24.1) WILD-TYPE 
                             4                             12 
$`DEL PEAK 11(10Q24.1) MUTATED`
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BD TCGA-SH-A7BH 
       17.33         3.52        13.61         0.23        15.09         7.99 

$`DEL PEAK 11(10Q24.1) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BN 
       91.73        18.81        23.31         5.19        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SH-A7BC 
       43.27        51.78        23.90 

  DEL PEAK 11(10Q24.1) MUTATED DEL PEAK 11(10Q24.1) WILD-TYPE 
                          0.23                           1.87 
  DEL PEAK 11(10Q24.1) MUTATED DEL PEAK 11(10Q24.1) WILD-TYPE 
                         17.33                          91.73 
  DEL PEAK 11(10Q24.1) MUTATED DEL PEAK 11(10Q24.1) WILD-TYPE 
                         10.80                          23.31 
[1] "0.2 - 17.3 (10.8)" "1.9 - 91.7 (23.3)"
[1] "hr=" "4.1"
D14V2, continuous
                                vv
clus                             STAGE I STAGE IB STAGE II STAGE III STAGE IV
  DEL PEAK 11(10Q24.1) MUTATED         0        1        1         3        1
  DEL PEAK 11(10Q24.1) WILD-TYPE       1        0        5         8        1
D14V3, multiclass
           clus
vv          DEL PEAK 11(10Q24.1) MUTATED DEL PEAK 11(10Q24.1) WILD-TYPE
  STAGE I                              0                              1
  STAGE IB                             1                              0
  STAGE II                             1                              5
  STAGE III                            3                              8
  STAGE IV                             1                              1
[1] 5 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(10Q24.1) MUTATED       3     3
  DEL PEAK 11(10Q24.1) WILD-TYPE    10     5
D14V4, multiclass
       clus
vv      DEL PEAK 11(10Q24.1) MUTATED DEL PEAK 11(10Q24.1) WILD-TYPE
  T1+T2                            3                             10
  T3+T4                            3                              5
[1] 2 2
[1] FALSE
                                vv
clus                             N0 N1+N2
  DEL PEAK 11(10Q24.1) MUTATED    5     0
  DEL PEAK 11(10Q24.1) WILD-TYPE  9     6
D14V5, multiclass
       clus
vv      DEL PEAK 11(10Q24.1) MUTATED DEL PEAK 11(10Q24.1) WILD-TYPE
  N0                               5                              9
  N1+N2                            0                              6
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 11(10Q24.1) MUTATED    3  1  2
  DEL PEAK 11(10Q24.1) WILD-TYPE 12  0  3
D14V6, multiclass
    clus
vv   DEL PEAK 11(10Q24.1) MUTATED DEL PEAK 11(10Q24.1) WILD-TYPE
  M0                            3                             12
  M1                            1                              0
  MX                            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"
D14V7, binary
                                cls
clus                              0  1
  DEL PEAK 11(10Q24.1) MUTATED    1  5
  DEL PEAK 11(10Q24.1) WILD-TYPE  5 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(10Q24.1) MUTATED      1    5
  DEL PEAK 11(10Q24.1) WILD-TYPE    5   10
        clus
vv       DEL PEAK 11(10Q24.1) MUTATED DEL PEAK 11(10Q24.1) WILD-TYPE
  FEMALE                            1                              5
  MALE                              5                             10
[1] 2 2
[1] FALSE

Clustering(15) Variable = DEL PEAK 12(13Q13.3) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 12(13Q13.3) MUTATED    2 13
  DEL PEAK 12(13Q13.3) WILD-TYPE  3  3
  DEL PEAK 12(13Q13.3) MUTATED DEL PEAK 12(13Q13.3) WILD-TYPE 
                            15                              6 
  DEL PEAK 12(13Q13.3) MUTATED DEL PEAK 12(13Q13.3) WILD-TYPE 
                            13                              3 
$`DEL PEAK 12(13Q13.3) MUTATED`
TCGA-LK-A4NW TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       17.95         1.87        12.20        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BS 
       23.31         5.19        17.33         3.52        10.95        13.61 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       23.90        15.09         7.99 

$`DEL PEAK 12(13Q13.3) WILD-TYPE`
TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I 
        8.02        31.20        24.89        43.27        51.78         0.23 

  DEL PEAK 12(13Q13.3) MUTATED DEL PEAK 12(13Q13.3) WILD-TYPE 
                          1.87                           0.23 
  DEL PEAK 12(13Q13.3) MUTATED DEL PEAK 12(13Q13.3) WILD-TYPE 
                         91.73                          51.78 
  DEL PEAK 12(13Q13.3) MUTATED DEL PEAK 12(13Q13.3) WILD-TYPE 
                        15.090                         28.045 
[1] "1.9 - 91.7 (15.1)" "0.2 - 51.8 (28.0)"
[1] "hr=" "2.6"
D15V2, continuous
                                vv
clus                             STAGE I STAGE IB STAGE II STAGE III STAGE IV
  DEL PEAK 12(13Q13.3) MUTATED         1        0        4         8        2
  DEL PEAK 12(13Q13.3) WILD-TYPE       0        1        2         3        0
D15V3, multiclass
           clus
vv          DEL PEAK 12(13Q13.3) MUTATED DEL PEAK 12(13Q13.3) WILD-TYPE
  STAGE I                              1                              0
  STAGE IB                             0                              1
  STAGE II                             4                              2
  STAGE III                            8                              3
  STAGE IV                             2                              0
[1] 5 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(13Q13.3) MUTATED       7     8
  DEL PEAK 12(13Q13.3) WILD-TYPE     6     0
D15V4, multiclass
       clus
vv      DEL PEAK 12(13Q13.3) MUTATED DEL PEAK 12(13Q13.3) WILD-TYPE
  T1+T2                            7                              6
  T3+T4                            8                              0
[1] 2 2
[1] FALSE
                                vv
clus                             N0 N1+N2
  DEL PEAK 12(13Q13.3) MUTATED   12     3
  DEL PEAK 12(13Q13.3) WILD-TYPE  2     3
D15V5, multiclass
       clus
vv      DEL PEAK 12(13Q13.3) MUTATED DEL PEAK 12(13Q13.3) WILD-TYPE
  N0                              12                              2
  N1+N2                            3                              3
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 12(13Q13.3) MUTATED   13  1  1
  DEL PEAK 12(13Q13.3) WILD-TYPE  2  0  4
D15V6, multiclass
    clus
vv   DEL PEAK 12(13Q13.3) MUTATED DEL PEAK 12(13Q13.3) WILD-TYPE
  M0                           13                              2
  M1                            1                              0
  MX                            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"
D15V7, binary
                                cls
clus                              0  1
  DEL PEAK 12(13Q13.3) MUTATED    4 11
  DEL PEAK 12(13Q13.3) WILD-TYPE  2  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(13Q13.3) MUTATED      4   11
  DEL PEAK 12(13Q13.3) WILD-TYPE    2    4
        clus
vv       DEL PEAK 12(13Q13.3) MUTATED DEL PEAK 12(13Q13.3) WILD-TYPE
  FEMALE                            4                              2
  MALE                             11                              4
[1] 2 2
[1] FALSE

Clustering(16) Variable = DEL PEAK 13(14Q11.2) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 13(14Q11.2) MUTATED    2  5
  DEL PEAK 13(14Q11.2) WILD-TYPE  3 11
  DEL PEAK 13(14Q11.2) MUTATED DEL PEAK 13(14Q11.2) WILD-TYPE 
                             7                             14 
  DEL PEAK 13(14Q11.2) MUTATED DEL PEAK 13(14Q11.2) WILD-TYPE 
                             5                             11 
$`DEL PEAK 13(14Q11.2) MUTATED`
TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BS TCGA-SH-A7BC 
        1.87        12.20        18.81        23.31        13.61        23.90 
TCGA-SH-A7BH 
        7.99 

$`DEL PEAK 13(14Q11.2) 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-A6BQ TCGA-MQ-A6BR 
       17.33         3.52        10.95        24.89        43.27        51.78 
TCGA-NQ-A57I TCGA-SH-A7BD 
        0.23        15.09 

  DEL PEAK 13(14Q11.2) MUTATED DEL PEAK 13(14Q11.2) WILD-TYPE 
                          1.87                           0.23 
  DEL PEAK 13(14Q11.2) MUTATED DEL PEAK 13(14Q11.2) WILD-TYPE 
                         23.90                          91.73 
  DEL PEAK 13(14Q11.2) MUTATED DEL PEAK 13(14Q11.2) WILD-TYPE 
                         13.61                          17.64 
[1] "1.9 - 23.9 (13.6)" "0.2 - 91.7 (17.6)"
[1] "hr=" "1.7"
D16V2, continuous
                                vv
clus                             STAGE I STAGE IB STAGE II STAGE III STAGE IV
  DEL PEAK 13(14Q11.2) MUTATED         0        0        2         5        0
  DEL PEAK 13(14Q11.2) WILD-TYPE       1        1        4         6        2
D16V3, multiclass
           clus
vv          DEL PEAK 13(14Q11.2) MUTATED DEL PEAK 13(14Q11.2) WILD-TYPE
  STAGE I                              0                              1
  STAGE IB                             0                              1
  STAGE II                             2                              4
  STAGE III                            5                              6
  STAGE IV                             0                              2
[1] 5 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(14Q11.2) MUTATED       3     4
  DEL PEAK 13(14Q11.2) WILD-TYPE    10     4
D16V4, multiclass
       clus
vv      DEL PEAK 13(14Q11.2) MUTATED DEL PEAK 13(14Q11.2) WILD-TYPE
  T1+T2                            3                             10
  T3+T4                            4                              4
[1] 2 2
[1] FALSE
                                vv
clus                             N0 N1+N2
  DEL PEAK 13(14Q11.2) MUTATED    5     2
  DEL PEAK 13(14Q11.2) WILD-TYPE  9     4
D16V5, multiclass
       clus
vv      DEL PEAK 13(14Q11.2) MUTATED DEL PEAK 13(14Q11.2) WILD-TYPE
  N0                               5                              9
  N1+N2                            2                              4
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 13(14Q11.2) MUTATED    6  0  1
  DEL PEAK 13(14Q11.2) WILD-TYPE  9  1  4
D16V6, multiclass
    clus
vv   DEL PEAK 13(14Q11.2) MUTATED DEL PEAK 13(14Q11.2) WILD-TYPE
  M0                            6                              9
  M1                            0                              1
  MX                            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"
D16V7, binary
                                cls
clus                              0  1
  DEL PEAK 13(14Q11.2) MUTATED    4  3
  DEL PEAK 13(14Q11.2) WILD-TYPE  2 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(14Q11.2) MUTATED      4    3
  DEL PEAK 13(14Q11.2) WILD-TYPE    2   12
        clus
vv       DEL PEAK 13(14Q11.2) MUTATED DEL PEAK 13(14Q11.2) WILD-TYPE
  FEMALE                            4                              2
  MALE                              3                             12
[1] 2 2
[1] FALSE

Clustering(17) Variable = DEL PEAK 14(14Q32.31) MUTATION ANALYSIS
D17V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 14(14Q32.31) MUTATED    3  5
  DEL PEAK 14(14Q32.31) WILD-TYPE  2 11
  DEL PEAK 14(14Q32.31) MUTATED DEL PEAK 14(14Q32.31) WILD-TYPE 
                              8                              13 
  DEL PEAK 14(14Q32.31) MUTATED DEL PEAK 14(14Q32.31) WILD-TYPE 
                              5                              11 
$`DEL PEAK 14(14Q32.31) MUTATED`
TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BQ TCGA-MQ-A6BS 
        1.87        12.20        18.81        23.31        43.27        13.61 
TCGA-SH-A7BC TCGA-SH-A7BH 
       23.90         7.99 

$`DEL PEAK 14(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-SH-A7BD 
       15.09 

  DEL PEAK 14(14Q32.31) MUTATED DEL PEAK 14(14Q32.31) WILD-TYPE 
                           1.87                            0.23 
  DEL PEAK 14(14Q32.31) MUTATED DEL PEAK 14(14Q32.31) WILD-TYPE 
                          43.27                           91.73 
  DEL PEAK 14(14Q32.31) MUTATED DEL PEAK 14(14Q32.31) WILD-TYPE 
                          16.21                           17.33 
[1] "1.9 - 43.3 (16.2)" "0.2 - 91.7 (17.3)"
[1] "hr=" "1"  
D17V2, continuous
                                 vv
clus                              STAGE I STAGE IB STAGE II STAGE III STAGE IV
  DEL PEAK 14(14Q32.31) MUTATED         0        0        3         5        0
  DEL PEAK 14(14Q32.31) WILD-TYPE       1        1        3         6        2
D17V3, multiclass
           clus
vv          DEL PEAK 14(14Q32.31) MUTATED DEL PEAK 14(14Q32.31) WILD-TYPE
  STAGE I                               0                               1
  STAGE IB                              0                               1
  STAGE II                              3                               3
  STAGE III                             5                               6
  STAGE IV                              0                               2
[1] 5 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(14Q32.31) MUTATED       4     4
  DEL PEAK 14(14Q32.31) WILD-TYPE     9     4
D17V4, multiclass
       clus
vv      DEL PEAK 14(14Q32.31) MUTATED DEL PEAK 14(14Q32.31) WILD-TYPE
  T1+T2                             4                               9
  T3+T4                             4                               4
[1] 2 2
[1] FALSE
                                 vv
clus                              N0 N1+N2
  DEL PEAK 14(14Q32.31) MUTATED    6     2
  DEL PEAK 14(14Q32.31) WILD-TYPE  8     4
D17V5, multiclass
       clus
vv      DEL PEAK 14(14Q32.31) MUTATED DEL PEAK 14(14Q32.31) WILD-TYPE
  N0                                6                               8
  N1+N2                             2                               4
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  DEL PEAK 14(14Q32.31) MUTATED    6  0  2
  DEL PEAK 14(14Q32.31) WILD-TYPE  9  1  3
D17V6, multiclass
    clus
vv   DEL PEAK 14(14Q32.31) MUTATED DEL PEAK 14(14Q32.31) WILD-TYPE
  M0                             6                               9
  M1                             0                               1
  MX                             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"
D17V7, binary
                                 cls
clus                               0  1
  DEL PEAK 14(14Q32.31) MUTATED    4  4
  DEL PEAK 14(14Q32.31) WILD-TYPE  2 11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 14(14Q32.31) MUTATED      4    4
  DEL PEAK 14(14Q32.31) WILD-TYPE    2   11
        clus
vv       DEL PEAK 14(14Q32.31) MUTATED DEL PEAK 14(14Q32.31) WILD-TYPE
  FEMALE                             4                               2
  MALE                               4                              11
[1] 2 2
[1] FALSE

Clustering(18) Variable = DEL PEAK 15(15Q15.1) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 15(15Q15.1) MUTATED    2  6
  DEL PEAK 15(15Q15.1) WILD-TYPE  3 10
  DEL PEAK 15(15Q15.1) MUTATED DEL PEAK 15(15Q15.1) WILD-TYPE 
                             8                             13 
  DEL PEAK 15(15Q15.1) MUTATED DEL PEAK 15(15Q15.1) WILD-TYPE 
                             6                             10 
$`DEL PEAK 15(15Q15.1) MUTATED`
TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BS TCGA-NQ-A57I 
       23.31        17.33         3.52        24.89        13.61         0.23 
TCGA-SH-A7BC TCGA-SH-A7BH 
       23.90         7.99 

$`DEL PEAK 15(15Q15.1) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       91.73        18.81         5.19        10.95        43.27        51.78 
TCGA-SH-A7BD 
       15.09 

  DEL PEAK 15(15Q15.1) MUTATED DEL PEAK 15(15Q15.1) WILD-TYPE 
                          0.23                           1.87 
  DEL PEAK 15(15Q15.1) MUTATED DEL PEAK 15(15Q15.1) WILD-TYPE 
                         24.89                          91.73 
  DEL PEAK 15(15Q15.1) MUTATED DEL PEAK 15(15Q15.1) WILD-TYPE 
                         15.47                          17.95 
[1] "0.2 - 24.9 (15.5)" "1.9 - 91.7 (17.9)"
[1] "hr=" "1.8"
D18V2, continuous
                                vv
clus                             STAGE I STAGE IB STAGE II STAGE III STAGE IV
  DEL PEAK 15(15Q15.1) MUTATED         0        1        1         6        0
  DEL PEAK 15(15Q15.1) WILD-TYPE       1        0        5         5        2
D18V3, multiclass
           clus
vv          DEL PEAK 15(15Q15.1) MUTATED DEL PEAK 15(15Q15.1) WILD-TYPE
  STAGE I                              0                              1
  STAGE IB                             1                              0
  STAGE II                             1                              5
  STAGE III                            6                              5
  STAGE IV                             0                              2
[1] 5 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(15Q15.1) MUTATED       4     4
  DEL PEAK 15(15Q15.1) WILD-TYPE     9     4
D18V4, multiclass
       clus
vv      DEL PEAK 15(15Q15.1) MUTATED DEL PEAK 15(15Q15.1) WILD-TYPE
  T1+T2                            4                              9
  T3+T4                            4                              4
[1] 2 2
[1] FALSE
                                vv
clus                             N0 N1+N2
  DEL PEAK 15(15Q15.1) MUTATED    4     3
  DEL PEAK 15(15Q15.1) WILD-TYPE 10     3
D18V5, multiclass
       clus
vv      DEL PEAK 15(15Q15.1) MUTATED DEL PEAK 15(15Q15.1) WILD-TYPE
  N0                               4                             10
  N1+N2                            3                              3
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 15(15Q15.1) MUTATED    5  0  3
  DEL PEAK 15(15Q15.1) WILD-TYPE 10  1  2
D18V6, multiclass
    clus
vv   DEL PEAK 15(15Q15.1) MUTATED DEL PEAK 15(15Q15.1) WILD-TYPE
  M0                            5                             10
  M1                            0                              1
  MX                            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"
D18V7, binary
                                cls
clus                             0 1
  DEL PEAK 15(15Q15.1) MUTATED   2 6
  DEL PEAK 15(15Q15.1) WILD-TYPE 4 9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(15Q15.1) MUTATED      2    6
  DEL PEAK 15(15Q15.1) WILD-TYPE    4    9
        clus
vv       DEL PEAK 15(15Q15.1) MUTATED DEL PEAK 15(15Q15.1) WILD-TYPE
  FEMALE                            2                              4
  MALE                              6                              9
[1] 2 2
[1] FALSE

Clustering(19) Variable = DEL PEAK 17(16Q21) MUTATION ANALYSIS
D19V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 17(16Q21) MUTATED    1  5
  DEL PEAK 17(16Q21) WILD-TYPE  4 11
  DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE 
                           6                           15 
  DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE 
                           5                           11 
$`DEL PEAK 17(16Q21) MUTATED`
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BS 
       18.81        23.31         5.19        17.33         3.52        13.61 

$`DEL PEAK 17(16Q21) WILD-TYPE`
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX 
       17.95         8.02         1.87        31.20        12.20        80.84 
TCGA-MQ-A4LC TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I 
       91.73        10.95        24.89        43.27        51.78         0.23 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       23.90        15.09         7.99 

  DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE 
                        3.52                         0.23 
  DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE 
                       23.31                        91.73 
  DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE 
                       15.47                        17.95 
[1] "3.5 - 23.3 (15.5)" "0.2 - 91.7 (17.9)"
[1] "hr=" "2.6"
D19V2, continuous
                              vv
clus                           STAGE I STAGE IB STAGE II STAGE III STAGE IV
  DEL PEAK 17(16Q21) MUTATED         0        0        2         4        0
  DEL PEAK 17(16Q21) WILD-TYPE       1        1        4         7        2
D19V3, multiclass
           clus
vv          DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE
  STAGE I                            0                            1
  STAGE IB                           0                            1
  STAGE II                           2                            4
  STAGE III                          4                            7
  STAGE IV                           0                            2
[1] 5 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(16Q21) MUTATED       3     3
  DEL PEAK 17(16Q21) WILD-TYPE    10     5
D19V4, multiclass
       clus
vv      DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE
  T1+T2                          3                           10
  T3+T4                          3                            5
[1] 2 2
[1] FALSE
                              vv
clus                           N0 N1+N2
  DEL PEAK 17(16Q21) MUTATED    5     1
  DEL PEAK 17(16Q21) WILD-TYPE  9     5
D19V5, multiclass
       clus
vv      DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE
  N0                             5                            9
  N1+N2                          1                            5
[1] 2 2
[1] FALSE
                              vv
clus                           M0 M1 MX
  DEL PEAK 17(16Q21) MUTATED    5  0  1
  DEL PEAK 17(16Q21) WILD-TYPE 10  1  4
D19V6, multiclass
    clus
vv   DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE
  M0                          5                           10
  M1                          0                            1
  MX                          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"
D19V7, binary
                              cls
clus                            0  1
  DEL PEAK 17(16Q21) MUTATED    1  5
  DEL PEAK 17(16Q21) WILD-TYPE  5 10
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 17(16Q21) MUTATED      1    5
  DEL PEAK 17(16Q21) WILD-TYPE    5   10
        clus
vv       DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE
  FEMALE                          1                            5
  MALE                            5                           10
[1] 2 2
[1] FALSE

Clustering(20) Variable = DEL PEAK 18(16Q24.1) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(16Q24.1) MUTATED    1  5
  DEL PEAK 18(16Q24.1) WILD-TYPE  4 11
  DEL PEAK 18(16Q24.1) MUTATED DEL PEAK 18(16Q24.1) WILD-TYPE 
                             6                             15 
  DEL PEAK 18(16Q24.1) MUTATED DEL PEAK 18(16Q24.1) WILD-TYPE 
                             5                             11 
$`DEL PEAK 18(16Q24.1) MUTATED`
TCGA-LK-A4NW TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BS 
       17.95        18.81        23.31        17.33         3.52        13.61 

$`DEL PEAK 18(16Q24.1) WILD-TYPE`
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        8.02         1.87        31.20        12.20        80.84        91.73 
TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I 
        5.19        10.95        24.89        43.27        51.78         0.23 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       23.90        15.09         7.99 

  DEL PEAK 18(16Q24.1) MUTATED DEL PEAK 18(16Q24.1) WILD-TYPE 
                          3.52                           0.23 
  DEL PEAK 18(16Q24.1) MUTATED DEL PEAK 18(16Q24.1) WILD-TYPE 
                         23.31                          91.73 
  DEL PEAK 18(16Q24.1) MUTATED DEL PEAK 18(16Q24.1) WILD-TYPE 
                         17.64                          15.09 
[1] "3.5 - 23.3 (17.6)" "0.2 - 91.7 (15.1)"
[1] "hr=" "2.1"
D20V2, continuous
                                vv
clus                             STAGE I STAGE IB STAGE II STAGE III STAGE IV
  DEL PEAK 18(16Q24.1) MUTATED         0        0        2         3        1
  DEL PEAK 18(16Q24.1) WILD-TYPE       1        1        4         8        1
D20V3, multiclass
           clus
vv          DEL PEAK 18(16Q24.1) MUTATED DEL PEAK 18(16Q24.1) WILD-TYPE
  STAGE I                              0                              1
  STAGE IB                             0                              1
  STAGE II                             2                              4
  STAGE III                            3                              8
  STAGE IV                             1                              1
[1] 5 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(16Q24.1) MUTATED       3     3
  DEL PEAK 18(16Q24.1) WILD-TYPE    10     5
D20V4, multiclass
       clus
vv      DEL PEAK 18(16Q24.1) MUTATED DEL PEAK 18(16Q24.1) WILD-TYPE
  T1+T2                            3                             10
  T3+T4                            3                              5
[1] 2 2
[1] FALSE
                                vv
clus                             N0 N1+N2
  DEL PEAK 18(16Q24.1) MUTATED    4     2
  DEL PEAK 18(16Q24.1) WILD-TYPE 10     4
D20V5, multiclass
       clus
vv      DEL PEAK 18(16Q24.1) MUTATED DEL PEAK 18(16Q24.1) WILD-TYPE
  N0                               4                             10
  N1+N2                            2                              4
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 18(16Q24.1) MUTATED    5  0  1
  DEL PEAK 18(16Q24.1) WILD-TYPE 10  1  4
D20V6, multiclass
    clus
vv   DEL PEAK 18(16Q24.1) MUTATED DEL PEAK 18(16Q24.1) WILD-TYPE
  M0                            5                             10
  M1                            0                              1
  MX                            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"
D20V7, binary
                                cls
clus                              0  1
  DEL PEAK 18(16Q24.1) MUTATED    1  5
  DEL PEAK 18(16Q24.1) WILD-TYPE  5 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(16Q24.1) MUTATED      1    5
  DEL PEAK 18(16Q24.1) WILD-TYPE    5   10
        clus
vv       DEL PEAK 18(16Q24.1) MUTATED DEL PEAK 18(16Q24.1) WILD-TYPE
  FEMALE                            1                              5
  MALE                              5                             10
[1] 2 2
[1] FALSE

Clustering(21) Variable = DEL PEAK 19(22Q12.2) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 19(22Q12.2) MUTATED    4 11
  DEL PEAK 19(22Q12.2) WILD-TYPE  1  5
  DEL PEAK 19(22Q12.2) MUTATED DEL PEAK 19(22Q12.2) WILD-TYPE 
                            15                              6 
  DEL PEAK 19(22Q12.2) MUTATED DEL PEAK 19(22Q12.2) WILD-TYPE 
                            11                              5 
$`DEL PEAK 19(22Q12.2) MUTATED`
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        8.02         1.87        12.20        91.73        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS 
        5.19        17.33         3.52        24.89        43.27        13.61 
TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BD 
        0.23        23.90        15.09 

$`DEL PEAK 19(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 

  DEL PEAK 19(22Q12.2) MUTATED DEL PEAK 19(22Q12.2) WILD-TYPE 
                          0.23                           7.99 
  DEL PEAK 19(22Q12.2) MUTATED DEL PEAK 19(22Q12.2) WILD-TYPE 
                         91.73                          80.84 
  DEL PEAK 19(22Q12.2) MUTATED DEL PEAK 19(22Q12.2) WILD-TYPE 
                        15.090                         24.575 
[1] "0.2 - 91.7 (15.1)" "8.0 - 80.8 (24.6)"
[1] "hr=" "1.3"
D21V2, continuous
                                vv
clus                             STAGE I STAGE IB STAGE II STAGE III STAGE IV
  DEL PEAK 19(22Q12.2) MUTATED         0        1        5         8        1
  DEL PEAK 19(22Q12.2) WILD-TYPE       1        0        1         3        1
D21V3, multiclass
           clus
vv          DEL PEAK 19(22Q12.2) MUTATED DEL PEAK 19(22Q12.2) WILD-TYPE
  STAGE I                              0                              1
  STAGE IB                             1                              0
  STAGE II                             5                              1
  STAGE III                            8                              3
  STAGE IV                             1                              1
[1] 5 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(22Q12.2) MUTATED       9     6
  DEL PEAK 19(22Q12.2) WILD-TYPE     4     2
D21V4, multiclass
       clus
vv      DEL PEAK 19(22Q12.2) MUTATED DEL PEAK 19(22Q12.2) WILD-TYPE
  T1+T2                            9                              4
  T3+T4                            6                              2
[1] 2 2
[1] FALSE
                                vv
clus                             N0 N1+N2
  DEL PEAK 19(22Q12.2) MUTATED   11     3
  DEL PEAK 19(22Q12.2) WILD-TYPE  3     3
D21V5, multiclass
       clus
vv      DEL PEAK 19(22Q12.2) MUTATED DEL PEAK 19(22Q12.2) WILD-TYPE
  N0                              11                              3
  N1+N2                            3                              3
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 19(22Q12.2) MUTATED   10  1  4
  DEL PEAK 19(22Q12.2) WILD-TYPE  5  0  1
D21V6, multiclass
    clus
vv   DEL PEAK 19(22Q12.2) MUTATED DEL PEAK 19(22Q12.2) WILD-TYPE
  M0                           10                              5
  M1                            1                              0
  MX                            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"
D21V7, binary
                                cls
clus                              0  1
  DEL PEAK 19(22Q12.2) MUTATED    4 11
  DEL PEAK 19(22Q12.2) WILD-TYPE  2  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(22Q12.2) MUTATED      4   11
  DEL PEAK 19(22Q12.2) WILD-TYPE    2    4
        clus
vv       DEL PEAK 19(22Q12.2) MUTATED DEL PEAK 19(22Q12.2) WILD-TYPE
  FEMALE                            4                              2
  MALE                             11                              4
[1] 2 2
[1] FALSE
