[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/15084766/MESO-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/MESO-TP/15089884/transformed.cor.cli.txt"

nPatients in clinical file=77, in cluster file=87, common to both=77
[1] 21 77
[1] "DEL PEAK  1(1P36.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            32                             45 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            32                             45 
[1] "DEL PEAK  2(1P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                           34                            43 
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                           34                            43 
[1] "DEL PEAK  3(2Q35) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                         15                          62 
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                         15                          62 
[1] "DEL PEAK  4(3P21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                           41                            36 
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                           41                            36 
[1] "DEL PEAK  5(4Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                         35                          42 
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                         35                          42 
[1] "DEL PEAK  6(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           38                            39 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           38                            39 
[1] "DEL PEAK  7(5Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE 
                           15                            62 
  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE 
                           15                            62 
[1] "DEL PEAK  8(6Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE 
                           37                            40 
  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE 
                           37                            40 
[1] "DEL PEAK  9(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                         32                          45 
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                         32                          45 
[1] "DEL PEAK 10(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                           16                            61 
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                           16                            61 
[1] "DEL PEAK 11(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                           48                            29 
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                           48                            29 
[1] "DEL PEAK 12(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                            26                             51 
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                            26                             51 
[1] "DEL PEAK 13(10Q25.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                            28                             49 
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                            28                             49 
[1] "DEL PEAK 14(11Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE 
                            16                             61 
  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE 
                            16                             61 
[1] "DEL PEAK 15(12P13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE 
                              9                              68 
  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE 
                              9                              68 
[1] "DEL PEAK 16(13Q14.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE 
                             41                              36 
  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE 
                             41                              36 
[1] "DEL PEAK 17(14Q32.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE 
                             36                              41 
  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE 
                             36                              41 
[1] "DEL PEAK 18(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE 
                            25                             52 
  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE 
                            25                             52 
[1] "DEL PEAK 19(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                             5                             72 
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                             5                             72 
[1] "DEL PEAK 20(16Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE 
                            20                             57 
  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE 
                            20                             57 
[1] "DEL PEAK 21(22Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE 
                            60                             17 
  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE 
                            60                             17 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "NEOPLASM_DISEASESTAGE"                 
 [6] "PATHOLOGY_T_STAGE"                     
 [7] "PATHOLOGY_N_STAGE"                     
 [8] "PATHOLOGY_M_STAGE"                     
 [9] "DCC_UPLOAD_DATE"                       
[10] "GENDER"                                
[11] "RADIATION_THERAPY"                     
[12] "KARNOFSKY_PERFORMANCE_SCORE"           
[13] "RADIATIONS_RADIATION_REGIMENINDICATION"
[14] "RACE"                                  
[15] "ETHNICITY"                             
[16] "BATCH_NUMBER"                          

Input Data has 16 rows and 77 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=63,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'NEOPLASM_DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 14:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RACE excluded in the analysis because there is no case of (both >= 3) in the table below"
              ASIAN   BLACK OR AFRICAN AMERICAN WHITE  
freq.values   "1"     "1"                       "75"   
freq.contrast "76"    "76"                      "2"    
both >= 3     "FALSE" "FALSE"                   "FALSE"
Variable 15:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'BATCH_NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 77 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"              "NEOPLASM_DISEASESTAGE"      
[3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
[5] "PATHOLOGY_M_STAGE"           "GENDER"                     
[7] "KARNOFSKY_PERFORMANCE_SCORE"
YEARS_TO_BIRTH, nv=34, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
14 25 28  8 
[1] "table(vv)"
vv
T1 T2 T3 T4 
14 25 28  8 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 T4 
14 25 28  8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
14 25 28  8 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
42 10 19  2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
   42    10    21 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 N3 
42 10 19  2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
   42    10    21 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=4, binary=FALSE, numeric=TRUE

Clustering(1) Variable = DEL PEAK  1(1P36.31) MUTATION ANALYSIS
D1V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.31) MUTATED    2 29
  DEL PEAK  1(1P36.31) WILD-TYPE  9 36
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            31                             45 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            29                             36 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-3H-AB3M TCGA-3H-AB3X TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       29.10        26.40         5.52         8.02         6.08         1.87 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A6BL 
       12.72        14.73        11.51        18.81         5.19        10.95 
TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A9CU TCGA-TS-A7OY TCGA-TS-A7OZ 
       19.99        13.61        23.90        14.76         8.38        27.75 
TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A8AF TCGA-TS-A8AI TCGA-UD-AAC4 TCGA-UD-AAC5 
       41.46         9.30        11.77        10.78        23.64         8.32 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88E TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       14.99        13.35        14.27         4.67         1.28         4.37 
TCGA-ZN-A9VW 
        2.76 

$`DEL PEAK  1(1P36.31) WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U 
       56.38        11.87        42.81        12.66        13.61        27.16 
TCGA-LK-A4NW TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LP 
       17.95        31.20        80.84        91.73        23.31        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM 
        3.52        24.89        66.54        62.27         0.66        28.96 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BD TCGA-SH-A7BH 
        2.56         9.76        29.42        17.72        15.09         7.99 
TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 
       14.76        55.07        18.51        22.65        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ 
       32.28        26.14         1.55        15.42        27.72         6.48 
TCGA-UD-AAC1 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88G TCGA-UT-A97Y TCGA-YS-AA4M 
       25.94        23.77        21.44         2.50         4.73         2.76 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
       16.41        33.70        24.30 

  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                          1.28                           0.66 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                         41.46                          91.73 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                         11.77                          19.43 
[1] "1.3 - 41.5 (11.8)" "0.7 - 91.7 (19.4)"
[1] "hr=" "2.4"
D1V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  1(1P36.31) MUTATED         2        1        0        7        17
  DEL PEAK  1(1P36.31) WILD-TYPE       5        1        1        9        23
                                vv
clus                             STAGE IV
  DEL PEAK  1(1P36.31) MUTATED          5
  DEL PEAK  1(1P36.31) WILD-TYPE        6
D1V3, multiclass
           clus
vv          DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  STAGE I                              2                              5
  STAGE IA                             1                              1
  STAGE IB                             0                              1
  STAGE II                             7                              9
  STAGE III                           17                             23
  STAGE IV                             5                              6
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK  1(1P36.31) MUTATED    4 10 14  4
  DEL PEAK  1(1P36.31) WILD-TYPE 10 15 14  4
D1V4, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  T1                            4                             10
  T2                           10                             15
  T3                           14                             14
  T4                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK  1(1P36.31) MUTATED   16  4    10
  DEL PEAK  1(1P36.31) WILD-TYPE 26  6    11
D1V5, multiclass
       clus
vv      DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  N0                              16                             26
  N1                               4                              6
  N2+N3                           10                             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.31) MUTATED   22  0
  DEL PEAK  1(1P36.31) WILD-TYPE 27  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     22    0
  DEL PEAK  1(1P36.31) WILD-TYPE   27    2
   clus
vv  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  0                           22                             27
  1                            0                              2
[1] 2 2
[1] FALSE
D1V7, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.31) MUTATED    7 25
  DEL PEAK  1(1P36.31) WILD-TYPE  8 37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      7   25
  DEL PEAK  1(1P36.31) WILD-TYPE    8   37
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  FEMALE                            7                              8
  MALE                             25                             37
[1] 2 2
[1] FALSE
D1V8, continuous
[1] "Remove cluster labels:"       "DEL PEAK  1(1P36.31) MUTATED"
clus
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                             1                              5 
                    TCGA-SC-A6LR                     TCGA-SH-A7BH 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-ZN-A9VQ                     TCGA-ZN-A9VS 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-ZN-A9VU 
"DEL PEAK  1(1P36.31) WILD-TYPE" 

Clustering(2) Variable = DEL PEAK  2(1P21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(1P21.3) MUTATED    1 33
  DEL PEAK  2(1P21.3) WILD-TYPE 10 32
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                           34                            42 
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                           33                            32 
$`DEL PEAK  2(1P21.3) MUTATED`
TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3S TCGA-3H-AB3T TCGA-LK-A4NY TCGA-LK-A4O0 
       56.38        29.10        12.66        13.61         5.52         6.08 
TCGA-LK-A4O2 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.87        14.73        11.51        91.73        18.81        23.31 
TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BD 
       17.33        10.95        19.99        28.96        13.61        15.09 
TCGA-SH-A9CT TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 
       14.76        27.75        18.51        22.65         9.30        19.43 
TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ 
       32.28        11.77        10.78        15.42        27.72         6.48 
TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88D TCGA-YS-A95B 
        8.32        13.35        21.44         1.28 

$`DEL PEAK  2(1P21.3) WILD-TYPE`
TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NZ 
       11.87        42.81        27.16        26.40        17.95         8.02 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BN 
       31.20        12.72        80.84         5.19         3.52        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR 
       66.54        62.27         0.66         2.56         9.76        29.42 
TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY 
       17.72        23.90         7.99        14.76        55.07         8.38 
TCGA-TS-A7P0 TCGA-TS-A7P8 TCGA-TS-A8AS TCGA-TS-A8AV TCGA-UD-AAC1 TCGA-UD-AAC4 
       41.46        15.02        26.14         1.55        25.94        23.64 
TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       14.99        23.77        14.27         2.50         4.73         4.67 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        4.37         2.76        16.41        33.70        24.30         2.76 

  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                         1.28                          0.66 
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                        91.73                         80.84 
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                       14.925                        15.715 
[1] "1.3 - 91.7 (14.9)" "0.7 - 80.8 (15.7)"
[1] "hr=" "1.4"
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  2(1P21.3) MUTATED         3        1        0       10        16
  DEL PEAK  2(1P21.3) WILD-TYPE       4        1        1        6        24
                               vv
clus                            STAGE IV
  DEL PEAK  2(1P21.3) MUTATED          4
  DEL PEAK  2(1P21.3) WILD-TYPE        7
D2V3, multiclass
           clus
vv          DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE
  STAGE I                             3                             4
  STAGE IA                            1                             1
  STAGE IB                            0                             1
  STAGE II                           10                             6
  STAGE III                          16                            24
  STAGE IV                            4                             7
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  2(1P21.3) MUTATED    4 14 13  3
  DEL PEAK  2(1P21.3) WILD-TYPE 10 11 15  5
D2V4, multiclass
    clus
vv   DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE
  T1                           4                            10
  T2                          14                            11
  T3                          13                            15
  T4                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK  2(1P21.3) MUTATED   19  6     8
  DEL PEAK  2(1P21.3) WILD-TYPE 23  4    13
D2V5, multiclass
       clus
vv      DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE
  N0                             19                            23
  N1                              6                             4
  N2+N3                           8                            13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P21.3) MUTATED   23  1
  DEL PEAK  2(1P21.3) WILD-TYPE 26  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P21.3) MUTATED     23    1
  DEL PEAK  2(1P21.3) WILD-TYPE   26    1
   clus
vv  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE
  0                          23                            26
  1                           1                             1
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P21.3) MUTATED    8 26
  DEL PEAK  2(1P21.3) WILD-TYPE  7 36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P21.3) MUTATED      8   26
  DEL PEAK  2(1P21.3) WILD-TYPE    7   36
        clus
vv       DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE
  FEMALE                           8                             7
  MALE                            26                            36
[1] 2 2
[1] FALSE
D2V8, continuous

Clustering(3) Variable = DEL PEAK  3(2Q35) MUTATION ANALYSIS
D3V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  3(2Q35) MUTATED    1 14
  DEL PEAK  3(2Q35) WILD-TYPE 10 51
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                         15                          61 
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                         14                          51 
$`DEL PEAK  3(2Q35) MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3S TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-LK-A4O2 
       11.87        29.10        12.66         5.52         6.08         1.87 
TCGA-LK-A4O5 TCGA-MQ-A4LI TCGA-SC-A6LQ TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7P1 
       12.72        18.81         9.76         7.99        14.76        18.51 
TCGA-TS-A7P6 TCGA-UD-AABY TCGA-UD-AAC7 
        9.30        27.72        13.35 

$`DEL PEAK  3(2Q35) WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3O TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW 
       56.38        42.81        13.61        27.16        26.40        17.95 
TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        8.02        31.20        14.73        11.51        80.84        91.73 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
       66.54        62.27        19.99         0.66        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT 
        2.56        29.42        17.72        23.90        15.09        14.76 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P3 TCGA-TS-A7P7 
       55.07         8.38        27.75        41.46        22.65        19.43 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV 
       15.02        32.28        11.77        10.78        26.14         1.55 
TCGA-TS-A8AY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 
       15.42         6.48        25.94        23.64         8.32        14.99 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       23.77        21.44        14.27         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        1.28         4.37         2.76        16.41        33.70        24.30 
TCGA-ZN-A9VW 
        2.76 

  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                       1.87                        0.66 
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                      29.10                       91.73 
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                      12.66                       17.33 
[1] "1.9 - 29.1 (12.7)" "0.7 - 91.7 (17.3)"
[1] "hr=" "1.9"
D3V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  3(2Q35) MUTATED         1        1        0        3         9
  DEL PEAK  3(2Q35) WILD-TYPE       6        1        1       13        31
                             vv
clus                          STAGE IV
  DEL PEAK  3(2Q35) MUTATED          1
  DEL PEAK  3(2Q35) WILD-TYPE       10
D3V3, multiclass
           clus
vv          DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  STAGE I                           1                           6
  STAGE IA                          1                           1
  STAGE IB                          0                           1
  STAGE II                          3                          13
  STAGE III                         9                          31
  STAGE IV                          1                          10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T1 T2 T3 T4
  DEL PEAK  3(2Q35) MUTATED    2  3  8  1
  DEL PEAK  3(2Q35) WILD-TYPE 12 22 20  7
D3V4, multiclass
    clus
vv   DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  T1                         2                          12
  T2                         3                          22
  T3                         8                          20
  T4                         1                           7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2+N3
  DEL PEAK  3(2Q35) MUTATED   10  0     5
  DEL PEAK  3(2Q35) WILD-TYPE 32 10    16
D3V5, multiclass
       clus
vv      DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  N0                           10                          32
  N1                            0                          10
  N2+N3                         5                          16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                             cls
clus                           0  1
  DEL PEAK  3(2Q35) MUTATED   13  0
  DEL PEAK  3(2Q35) WILD-TYPE 36  2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(2Q35) MUTATED     13    0
  DEL PEAK  3(2Q35) WILD-TYPE   36    2
   clus
vv  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  0                        13                          36
  1                         0                           2
[1] 2 2
[1] FALSE
D3V7, binary
                             cls
clus                           0  1
  DEL PEAK  3(2Q35) MUTATED    7  8
  DEL PEAK  3(2Q35) WILD-TYPE  8 54
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(2Q35) MUTATED      7    8
  DEL PEAK  3(2Q35) WILD-TYPE    8   54
        clus
vv       DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  FEMALE                         7                           8
  MALE                           8                          54
[1] 2 2
[1] FALSE
D3V8, continuous
[1] "Remove cluster labels:"    "DEL PEAK  3(2Q35) MUTATED"
clus
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                          1                           5 
                 TCGA-SC-A6LR                  TCGA-XT-AASU 
"DEL PEAK  3(2Q35) WILD-TYPE" "DEL PEAK  3(2Q35) WILD-TYPE" 
                 TCGA-ZN-A9VQ                  TCGA-ZN-A9VS 
"DEL PEAK  3(2Q35) WILD-TYPE" "DEL PEAK  3(2Q35) WILD-TYPE" 
                 TCGA-ZN-A9VU 
"DEL PEAK  3(2Q35) WILD-TYPE" 

Clustering(4) Variable = DEL PEAK  4(3P21.1) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(3P21.1) MUTATED    4 37
  DEL PEAK  4(3P21.1) WILD-TYPE  7 28
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                           41                            35 
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                           37                            28 
$`DEL PEAK  4(3P21.1) MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3S TCGA-3H-AB3T TCGA-LK-A4NW TCGA-LK-A4NZ 
       11.87        29.10        12.66        13.61        17.95         8.02 
TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        1.87        12.72        14.73        11.51        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        19.99 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A7BD TCGA-TS-A7OU 
        0.66        28.96         9.76        23.90        15.09        55.07 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-UD-AABZ 
       18.51        22.65        32.28        11.77        10.78         6.48 
TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E 
       23.64         8.32        14.99        13.35        23.77        14.27 
TCGA-XT-AASU TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        4.67        16.41        33.70        24.30         2.76 

$`DEL PEAK  4(3P21.1) WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3O TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NY TCGA-LK-A4O0 
       56.38        42.81        27.16        26.40         5.52         6.08 
TCGA-LK-A4O4 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LN 
       31.20        18.81        23.31        66.54        62.27        13.61 
TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU 
        2.56        29.42        17.72         7.99        14.76        14.76 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 
        8.38        27.75        41.46         9.30        19.43        15.02 
TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UT-A88D 
       26.14         1.55        15.42        27.72        25.94        21.44 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
        2.50         4.73         1.28         4.37         2.76 

  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                         0.66                          1.28 
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                        91.73                         66.54 
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                        14.73                         17.72 
[1] "0.7 - 91.7 (14.7)" "1.3 - 66.5 (17.7)"
[1] "hr=" "1.2"
D4V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  4(3P21.1) MUTATED         6        0        1        9        19
  DEL PEAK  4(3P21.1) WILD-TYPE       1        2        0        7        21
                               vv
clus                            STAGE IV
  DEL PEAK  4(3P21.1) MUTATED          6
  DEL PEAK  4(3P21.1) WILD-TYPE        5
D4V3, multiclass
           clus
vv          DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  STAGE I                             6                             1
  STAGE IA                            0                             2
  STAGE IB                            1                             0
  STAGE II                            9                             7
  STAGE III                          19                            21
  STAGE IV                            6                             5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  4(3P21.1) MUTATED    7 13 15  5
  DEL PEAK  4(3P21.1) WILD-TYPE  7 12 13  3
D4V4, multiclass
    clus
vv   DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  T1                           7                             7
  T2                          13                            12
  T3                          15                            13
  T4                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK  4(3P21.1) MUTATED   24  4    10
  DEL PEAK  4(3P21.1) WILD-TYPE 18  6    11
D4V5, multiclass
       clus
vv      DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  N0                             24                            18
  N1                              4                             6
  N2+N3                          10                            11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                               cls
clus                             0  1
  DEL PEAK  4(3P21.1) MUTATED   26  1
  DEL PEAK  4(3P21.1) WILD-TYPE 23  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P21.1) MUTATED     26    1
  DEL PEAK  4(3P21.1) WILD-TYPE   23    1
   clus
vv  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  0                          26                            23
  1                           1                             1
[1] 2 2
[1] FALSE
D4V7, binary
                               cls
clus                             0  1
  DEL PEAK  4(3P21.1) MUTATED    7 34
  DEL PEAK  4(3P21.1) WILD-TYPE  8 28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P21.1) MUTATED      7   34
  DEL PEAK  4(3P21.1) WILD-TYPE    8   28
        clus
vv       DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  FEMALE                           7                             8
  MALE                            34                            28
[1] 2 2
[1] FALSE
D4V8, continuous
[1] "Remove cluster labels:"        "DEL PEAK  4(3P21.1) WILD-TYPE"
clus
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                            4                             2 
                 TCGA-XT-AASU                  TCGA-ZN-A9VQ 
"DEL PEAK  4(3P21.1) MUTATED" "DEL PEAK  4(3P21.1) MUTATED" 
                 TCGA-ZN-A9VS                  TCGA-ZN-A9VU 
"DEL PEAK  4(3P21.1) MUTATED" "DEL PEAK  4(3P21.1) MUTATED" 

Clustering(5) Variable = DEL PEAK  5(4Q26) MUTATION ANALYSIS
D5V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  5(4Q26) MUTATED    3 32
  DEL PEAK  5(4Q26) WILD-TYPE  8 33
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                         35                          41 
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                         32                          33 
$`DEL PEAK  5(4Q26) MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 
       11.87        29.10        13.61         6.08         1.87        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
       14.73        11.51        18.81         5.19        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BH 
       10.95        62.27        19.99        13.61        23.90         7.99 
TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 
       14.76        14.76         8.38        27.75        41.46        18.51 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABZ 
        9.30        19.43        11.77        10.78        15.42         6.48 
TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88G TCGA-UT-A97Y TCGA-ZN-A9VS 
        8.32        13.35         2.50         4.73        33.70 

$`DEL PEAK  5(4Q26) WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW 
       56.38        42.81        12.66        27.16        26.40        17.95 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ 
        5.52         8.02        31.20        80.84        91.73        23.31 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LQ 
       24.89        66.54         0.66        28.96         2.56         9.76 
TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BD TCGA-TS-A7OU TCGA-TS-A7P3 TCGA-TS-A7P8 
       29.42        17.72        15.09        55.07        22.65        15.02 
TCGA-TS-A7PB TCGA-TS-A8AS TCGA-TS-A8AV TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC4 
       32.28        26.14         1.55        27.72        25.94        23.64 
TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-XT-AASU TCGA-YS-A95B 
       14.99        23.77        21.44        14.27         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VU TCGA-ZN-A9VW 
        4.37         2.76        16.41        24.30         2.76 

  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                       1.87                        0.66 
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                      62.27                       91.73 
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                      13.35                       22.65 
[1] "1.9 - 62.3 (13.3)" "0.7 - 91.7 (22.6)"
[1] "hr=" "1.9"
D5V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  5(4Q26) MUTATED         4        1        0        6        21
  DEL PEAK  5(4Q26) WILD-TYPE       3        1        1       10        19
                             vv
clus                          STAGE IV
  DEL PEAK  5(4Q26) MUTATED          3
  DEL PEAK  5(4Q26) WILD-TYPE        8
D5V3, multiclass
           clus
vv          DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  STAGE I                           4                           3
  STAGE IA                          1                           1
  STAGE IB                          0                           1
  STAGE II                          6                          10
  STAGE III                        21                          19
  STAGE IV                          3                           8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T1 T2 T3 T4
  DEL PEAK  5(4Q26) MUTATED    6  8 18  2
  DEL PEAK  5(4Q26) WILD-TYPE  8 17 10  6
D5V4, multiclass
    clus
vv   DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  T1                         6                           8
  T2                         8                          17
  T3                        18                          10
  T4                         2                           6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2+N3
  DEL PEAK  5(4Q26) MUTATED   20  6     9
  DEL PEAK  5(4Q26) WILD-TYPE 22  4    12
D5V5, multiclass
       clus
vv      DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  N0                           20                          22
  N1                            6                           4
  N2+N3                         9                          12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                             cls
clus                           0  1
  DEL PEAK  5(4Q26) MUTATED   23  0
  DEL PEAK  5(4Q26) WILD-TYPE 26  2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(4Q26) MUTATED     23    0
  DEL PEAK  5(4Q26) WILD-TYPE   26    2
   clus
vv  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  0                        23                          26
  1                         0                           2
[1] 2 2
[1] FALSE
D5V7, binary
                             cls
clus                           0  1
  DEL PEAK  5(4Q26) MUTATED    9 26
  DEL PEAK  5(4Q26) WILD-TYPE  6 36
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(4Q26) MUTATED      9   26
  DEL PEAK  5(4Q26) WILD-TYPE    6   36
        clus
vv       DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  FEMALE                         9                           6
  MALE                          26                          36
[1] 2 2
[1] FALSE
D5V8, continuous
[1] "Remove cluster labels:"    "DEL PEAK  5(4Q26) MUTATED"
clus
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                          2                           4 
                 TCGA-SC-A6LR                  TCGA-XT-AASU 
"DEL PEAK  5(4Q26) WILD-TYPE" "DEL PEAK  5(4Q26) WILD-TYPE" 
                 TCGA-ZN-A9VQ                  TCGA-ZN-A9VU 
"DEL PEAK  5(4Q26) WILD-TYPE" "DEL PEAK  5(4Q26) WILD-TYPE" 

Clustering(6) Variable = DEL PEAK  6(4Q34.3) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(4Q34.3) MUTATED    4 34
  DEL PEAK  6(4Q34.3) WILD-TYPE  7 31
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           38                            38 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           34                            31 
$`DEL PEAK  6(4Q34.3) MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T TCGA-3H-AB3X TCGA-LK-A4NY TCGA-LK-A4O0 
       11.87        29.10        13.61        26.40         5.52         6.08 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A4LP 
       12.72        14.73        11.51        18.81         5.19        17.33 
TCGA-MQ-A6BL TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BH 
       10.95        62.27        19.99        13.61        23.90         7.99 
TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P6 
       14.76        14.76         8.38        27.75        41.46         9.30 
TCGA-TS-A7P7 TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABZ TCGA-UD-AAC4 
       19.43        11.77        10.78        15.42         6.48        23.64 
TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
        8.32        14.99        13.35        14.27         2.50         4.73 
TCGA-ZN-A9VS TCGA-ZN-A9VW 
       33.70         2.76 

$`DEL PEAK  6(4Q34.3) WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3U TCGA-LK-A4NW TCGA-LK-A4NZ 
       56.38        42.81        12.66        27.16        17.95         8.02 
TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LV 
        1.87        31.20        80.84        91.73        23.31         3.52 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LQ 
       24.89        66.54         0.66        28.96         2.56         9.76 
TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BD TCGA-TS-A7OU TCGA-TS-A7P1 TCGA-TS-A7P3 
       29.42        17.72        15.09        55.07        18.51        22.65 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AS TCGA-TS-A8AV TCGA-UD-AABY TCGA-UD-AAC1 
       15.02        32.28        26.14         1.55        27.72        25.94 
TCGA-UT-A88C TCGA-UT-A88D TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
       23.77        21.44         4.67         1.28         4.37         2.76 
TCGA-ZN-A9VQ TCGA-ZN-A9VU 
       16.41        24.30 

  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                         2.50                          0.66 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                        62.27                         91.73 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                       13.610                        22.045 
[1] "2.5 - 62.3 (13.6)" "0.7 - 91.7 (22.0)"
[1] "hr=" "1.8"
D6V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  6(4Q34.3) MUTATED         4        1        0        7        22
  DEL PEAK  6(4Q34.3) WILD-TYPE       3        1        1        9        18
                               vv
clus                            STAGE IV
  DEL PEAK  6(4Q34.3) MUTATED          4
  DEL PEAK  6(4Q34.3) WILD-TYPE        7
D6V3, multiclass
           clus
vv          DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  STAGE I                             4                             3
  STAGE IA                            1                             1
  STAGE IB                            0                             1
  STAGE II                            7                             9
  STAGE III                          22                            18
  STAGE IV                            4                             7
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  6(4Q34.3) MUTATED    6 10 18  3
  DEL PEAK  6(4Q34.3) WILD-TYPE  8 15 10  5
D6V4, multiclass
    clus
vv   DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  T1                           6                             8
  T2                          10                            15
  T3                          18                            10
  T4                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK  6(4Q34.3) MUTATED   22  6    10
  DEL PEAK  6(4Q34.3) WILD-TYPE 20  4    11
D6V5, multiclass
       clus
vv      DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  N0                             22                            20
  N1                              6                             4
  N2+N3                          10                            11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q34.3) MUTATED   26  0
  DEL PEAK  6(4Q34.3) WILD-TYPE 23  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED     26    0
  DEL PEAK  6(4Q34.3) WILD-TYPE   23    2
   clus
vv  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  0                          26                            23
  1                           0                             2
[1] 2 2
[1] FALSE
D6V7, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q34.3) MUTATED    9 29
  DEL PEAK  6(4Q34.3) WILD-TYPE  6 33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED      9   29
  DEL PEAK  6(4Q34.3) WILD-TYPE    6   33
        clus
vv       DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  FEMALE                           9                             6
  MALE                            29                            33
[1] 2 2
[1] FALSE
D6V8, continuous
[1] "Remove cluster labels:"      "DEL PEAK  6(4Q34.3) MUTATED"
clus
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                            2                             4 
                   TCGA-SC-A6LR                    TCGA-XT-AASU 
"DEL PEAK  6(4Q34.3) WILD-TYPE" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-ZN-A9VQ                    TCGA-ZN-A9VU 
"DEL PEAK  6(4Q34.3) WILD-TYPE" "DEL PEAK  6(4Q34.3) WILD-TYPE" 

Clustering(7) Variable = DEL PEAK  7(5Q23.2) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  7(5Q23.2) MUTATED    1 14
  DEL PEAK  7(5Q23.2) WILD-TYPE 10 51
  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE 
                           15                            61 
  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE 
                           14                            51 
$`DEL PEAK  7(5Q23.2) MUTATED`
TCGA-3H-AB3L TCGA-LK-A4O7 TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SC-A6LQ 
       11.87        11.51         3.52        19.99        13.61         9.76 
TCGA-SH-A7BD TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A8AF TCGA-TS-A8AI 
       15.09        14.76        41.46        18.51        11.77        10.78 
TCGA-UD-AABZ TCGA-UD-AAC7 TCGA-XT-AASU 
        6.48        13.35         4.67 

$`DEL PEAK  7(5Q23.2) WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U 
       56.38        29.10        42.81        12.66        13.61        27.16 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       26.40        17.95         5.52         8.02         6.08         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       31.20        12.72        14.73        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       23.31         5.19        17.33        10.95        24.89        66.54 
TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SC-AA5Z 
       62.27         0.66        28.96         2.56        29.42        17.72 
TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
       23.90         7.99        14.76        55.07         8.38        27.75 
TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AS 
       22.65         9.30        19.43        15.02        32.28        26.14 
TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 
        1.55        15.42        27.72        25.94        23.64         8.32 
TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
       14.99        23.77        21.44        14.27         2.50         4.73 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        1.28         4.37         2.76        16.41        33.70        24.30 
TCGA-ZN-A9VW 
        2.76 

  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE 
                         3.52                          0.66 
  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE 
                        41.46                         91.73 
  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE 
                        11.87                         17.72 
[1] "3.5 - 41.5 (11.9)" "0.7 - 91.7 (17.7)"
[1] "hr=" "1.9"
D7V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  7(5Q23.2) MUTATED         1        0        0        3         8
  DEL PEAK  7(5Q23.2) WILD-TYPE       6        2        1       13        32
                               vv
clus                            STAGE IV
  DEL PEAK  7(5Q23.2) MUTATED          3
  DEL PEAK  7(5Q23.2) WILD-TYPE        8
D7V3, multiclass
           clus
vv          DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE
  STAGE I                             1                             6
  STAGE IA                            0                             2
  STAGE IB                            0                             1
  STAGE II                            3                            13
  STAGE III                           8                            32
  STAGE IV                            3                             8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  7(5Q23.2) MUTATED    1  6  5  2
  DEL PEAK  7(5Q23.2) WILD-TYPE 13 19 23  6
D7V4, multiclass
    clus
vv   DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE
  T1                           1                            13
  T2                           6                            19
  T3                           5                            23
  T4                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK  7(5Q23.2) MUTATED    7  2     5
  DEL PEAK  7(5Q23.2) WILD-TYPE 35  8    16
D7V5, multiclass
       clus
vv      DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE
  N0                              7                            35
  N1                              2                             8
  N2+N3                           5                            16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                               cls
clus                             0  1
  DEL PEAK  7(5Q23.2) MUTATED    8  1
  DEL PEAK  7(5Q23.2) WILD-TYPE 41  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5Q23.2) MUTATED      8    1
  DEL PEAK  7(5Q23.2) WILD-TYPE   41    1
   clus
vv  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE
  0                           8                            41
  1                           1                             1
[1] 2 2
[1] FALSE
D7V7, binary
                               cls
clus                             0  1
  DEL PEAK  7(5Q23.2) MUTATED    1 14
  DEL PEAK  7(5Q23.2) WILD-TYPE 14 48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5Q23.2) MUTATED      1   14
  DEL PEAK  7(5Q23.2) WILD-TYPE   14   48
        clus
vv       DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE
  FEMALE                           1                            14
  MALE                            14                            48
[1] 2 2
[1] FALSE
D7V8, continuous
[1] "Remove cluster labels:"      "DEL PEAK  7(5Q23.2) MUTATED"
clus
  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE 
                            1                             5 
                   TCGA-SC-A6LR                    TCGA-SH-A7BH 
"DEL PEAK  7(5Q23.2) WILD-TYPE" "DEL PEAK  7(5Q23.2) WILD-TYPE" 
                   TCGA-ZN-A9VQ                    TCGA-ZN-A9VS 
"DEL PEAK  7(5Q23.2) WILD-TYPE" "DEL PEAK  7(5Q23.2) WILD-TYPE" 
                   TCGA-ZN-A9VU 
"DEL PEAK  7(5Q23.2) WILD-TYPE" 

Clustering(8) Variable = DEL PEAK  8(6Q22.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(6Q22.1) MUTATED    5 31
  DEL PEAK  8(6Q22.1) WILD-TYPE  6 34
  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE 
                           36                            40 
  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE 
                           31                            34 
$`DEL PEAK  8(6Q22.1) MUTATED`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       56.38        11.87        29.10         8.02         6.08         1.87 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A4LV 
       11.51        80.84        91.73        18.81         5.19         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BC 
       10.95        24.89        66.54        19.99         0.66        23.90 
TCGA-SH-A7BD TCGA-SH-A9CU TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A7P7 
       15.09        14.76        27.75        41.46         9.30        19.43 
TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AY TCGA-UD-AAC5 TCGA-UD-AAC6 
       32.28        10.78        26.14        15.42         8.32        14.99 
TCGA-UD-AAC7 TCGA-UT-A88G TCGA-XT-AASU TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
       13.35         2.50         4.67        16.41        33.70        24.30 

$`DEL PEAK  8(6Q22.1) WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW 
       42.81        12.66        13.61        27.16        26.40        17.95 
TCGA-LK-A4NY TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4LJ TCGA-MQ-A4LP 
        5.52        31.20        12.72        14.73        23.31        17.33 
TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR 
       62.27        28.96        13.61         2.56         9.76        29.42 
TCGA-SC-AA5Z TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7P1 
       17.72         7.99        14.76        55.07         8.38        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P8 TCGA-TS-A8AF TCGA-TS-A8AV TCGA-UD-AABY TCGA-UD-AABZ 
       22.65        15.02        11.77         1.55        27.72         6.48 
TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A97Y 
       25.94        23.64        23.77        21.44        14.27         4.73 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VW 
        1.28         4.37         2.76         2.76 

  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE 
                         0.66                          1.28 
  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE 
                        91.73                         62.27 
  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE 
                       15.255                        14.890 
[1] "0.7 - 91.7 (15.3)" "1.3 - 62.3 (14.9)"
[1] "hr=" "1.2"
D8V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  8(6Q22.1) MUTATED         3        2        1       11        17
  DEL PEAK  8(6Q22.1) WILD-TYPE       4        0        0        5        23
                               vv
clus                            STAGE IV
  DEL PEAK  8(6Q22.1) MUTATED          3
  DEL PEAK  8(6Q22.1) WILD-TYPE        8
D8V3, multiclass
           clus
vv          DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE
  STAGE I                             3                             4
  STAGE IA                            2                             0
  STAGE IB                            1                             0
  STAGE II                           11                             5
  STAGE III                          17                            23
  STAGE IV                            3                             8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  8(6Q22.1) MUTATED    6 13 15  2
  DEL PEAK  8(6Q22.1) WILD-TYPE  8 12 13  6
D8V4, multiclass
    clus
vv   DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE
  T1                           6                             8
  T2                          13                            12
  T3                          15                            13
  T4                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK  8(6Q22.1) MUTATED   22  5     7
  DEL PEAK  8(6Q22.1) WILD-TYPE 20  5    14
D8V5, multiclass
       clus
vv      DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE
  N0                             22                            20
  N1                              5                             5
  N2+N3                           7                            14
[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"
D8V6, binary
                               cls
clus                             0  1
  DEL PEAK  8(6Q22.1) MUTATED   19  1
  DEL PEAK  8(6Q22.1) WILD-TYPE 30  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(6Q22.1) MUTATED     19    1
  DEL PEAK  8(6Q22.1) WILD-TYPE   30    1
   clus
vv  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE
  0                          19                            30
  1                           1                             1
[1] 2 2
[1] FALSE
D8V7, binary
                               cls
clus                             0  1
  DEL PEAK  8(6Q22.1) MUTATED    5 32
  DEL PEAK  8(6Q22.1) WILD-TYPE 10 30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(6Q22.1) MUTATED      5   32
  DEL PEAK  8(6Q22.1) WILD-TYPE   10   30
        clus
vv       DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE
  FEMALE                           5                            10
  MALE                            32                            30
[1] 2 2
[1] FALSE
D8V8, continuous
[1] "Remove cluster labels:"        "DEL PEAK  8(6Q22.1) WILD-TYPE"
clus
  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE 
                            4                             2 
                 TCGA-XT-AASU                  TCGA-ZN-A9VQ 
"DEL PEAK  8(6Q22.1) MUTATED" "DEL PEAK  8(6Q22.1) MUTATED" 
                 TCGA-ZN-A9VS                  TCGA-ZN-A9VU 
"DEL PEAK  8(6Q22.1) MUTATED" "DEL PEAK  8(6Q22.1) MUTATED" 

Clustering(9) Variable = DEL PEAK  9(6Q26) MUTATION ANALYSIS
D9V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  9(6Q26) MUTATED    4 27
  DEL PEAK  9(6Q26) WILD-TYPE  7 38
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                         31                          45 
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                         27                          38 
$`DEL PEAK  9(6Q26) MUTATED`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-LK-A4O2 
       56.38        11.87        29.10         5.52         6.08         1.87 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BQ 
       80.84        91.73        18.81         5.19        10.95        66.54 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A9CU 
       19.99         0.66        28.96        13.61        23.90        14.76 
TCGA-TS-A7OU TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-TS-A8AS 
       55.07        41.46         9.30        19.43        32.28        26.14 
TCGA-TS-A8AY TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88E TCGA-UT-A88G TCGA-ZN-A9VQ 
       15.42         8.32        13.35        14.27         2.50        16.41 
TCGA-ZN-A9VS 
       33.70 

$`DEL PEAK  9(6Q26) WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW 
       42.81        12.66        13.61        27.16        26.40        17.95 
TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LJ 
        8.02        31.20        12.72        14.73        11.51        23.31 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BR TCGA-SC-A6LP TCGA-SC-A6LQ 
       17.33         3.52        24.89        62.27         2.56         9.76 
TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OY 
       29.42        17.72        15.09         7.99        14.76         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P8 TCGA-TS-A8AF TCGA-TS-A8AI 
       27.75        18.51        22.65        15.02        11.77        10.78 
TCGA-TS-A8AV TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC6 
        1.55        27.72         6.48        25.94        23.64        14.99 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       23.77        21.44         4.73         4.67         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VU TCGA-ZN-A9VW 
        2.76        24.30         2.76 

  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                       0.66                        1.28 
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                      91.73                       62.27 
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                      16.41                       14.99 
[1] "0.7 - 91.7 (16.4)" "1.3 - 62.3 (15.0)"
[1] "hr=" "1.5"
D9V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  9(6Q26) MUTATED         4        2        1        8        14
  DEL PEAK  9(6Q26) WILD-TYPE       3        0        0        8        26
                             vv
clus                          STAGE IV
  DEL PEAK  9(6Q26) MUTATED          3
  DEL PEAK  9(6Q26) WILD-TYPE        8
D9V3, multiclass
           clus
vv          DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  STAGE I                           4                           3
  STAGE IA                          2                           0
  STAGE IB                          1                           0
  STAGE II                          8                           8
  STAGE III                        14                          26
  STAGE IV                          3                           8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T1 T2 T3 T4
  DEL PEAK  9(6Q26) MUTATED    7  9 12  3
  DEL PEAK  9(6Q26) WILD-TYPE  7 16 16  5
D9V4, multiclass
    clus
vv   DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  T1                         7                           7
  T2                         9                          16
  T3                        12                          16
  T4                         3                           5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2+N3
  DEL PEAK  9(6Q26) MUTATED   20  1     8
  DEL PEAK  9(6Q26) WILD-TYPE 22  9    13
D9V5, multiclass
       clus
vv      DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  N0                           20                          22
  N1                            1                           9
  N2+N3                         8                          13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                             cls
clus                           0  1
  DEL PEAK  9(6Q26) MUTATED   19  0
  DEL PEAK  9(6Q26) WILD-TYPE 30  2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(6Q26) MUTATED     19    0
  DEL PEAK  9(6Q26) WILD-TYPE   30    2
   clus
vv  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  0                        19                          30
  1                         0                           2
[1] 2 2
[1] FALSE
D9V7, binary
                             cls
clus                           0  1
  DEL PEAK  9(6Q26) MUTATED    6 26
  DEL PEAK  9(6Q26) WILD-TYPE  9 36
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(6Q26) MUTATED      6   26
  DEL PEAK  9(6Q26) WILD-TYPE    9   36
        clus
vv       DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  FEMALE                         6                           9
  MALE                          26                          36
[1] 2 2
[1] FALSE
D9V8, continuous
[1] "Remove cluster labels:"    "DEL PEAK  9(6Q26) MUTATED"
clus
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                          2                           4 
                 TCGA-SC-A6LR                  TCGA-SH-A7BH 
"DEL PEAK  9(6Q26) WILD-TYPE" "DEL PEAK  9(6Q26) WILD-TYPE" 
                 TCGA-XT-AASU                  TCGA-ZN-A9VU 
"DEL PEAK  9(6Q26) WILD-TYPE" "DEL PEAK  9(6Q26) WILD-TYPE" 

Clustering(10) Variable = DEL PEAK 10(8P23.2) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 10(8P23.2) MUTATED    3 13
  DEL PEAK 10(8P23.2) WILD-TYPE  8 52
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                           16                            60 
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                           13                            52 
$`DEL PEAK 10(8P23.2) MUTATED`
TCGA-3H-AB3K TCGA-LK-A4O0 TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A6BQ TCGA-MQ-A6BS 
       56.38         6.08        91.73        18.81        66.54        19.99 
TCGA-SC-A6LN TCGA-SC-A6LQ TCGA-SC-AA5Z TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OZ 
       13.61         9.76        17.72        14.76        55.07        27.75 
TCGA-TS-A7P1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-ZN-A9VW 
       18.51        23.64         8.32         2.76 

$`DEL PEAK 10(8P23.2) WILD-TYPE`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U 
       11.87        29.10        42.81        12.66        13.61        27.16 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 
       26.40        17.95         5.52         8.02         1.87        31.20 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       12.72        14.73        11.51        80.84        23.31         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        62.27         0.66 
TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       28.96         2.56        29.42        23.90        15.09         7.99 
TCGA-SH-A9CT TCGA-TS-A7OY TCGA-TS-A7P0 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 
       14.76         8.38        41.46        22.65         9.30        19.43 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV 
       15.02        32.28        11.77        10.78        26.14         1.55 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UD-AAC7 
       15.42        27.72         6.48        25.94        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       23.77        21.44        14.27         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        1.28         4.37         2.76        16.41        33.70        24.30 

  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                         2.76                          0.66 
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                        91.73                         80.84 
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                       18.660                        14.875 
[1] "2.8 - 91.7 (18.7)" "0.7 - 80.8 (14.9)"
[1] "hr=" "1.7"
D10V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 10(8P23.2) MUTATED         2        1        0        5         4
  DEL PEAK 10(8P23.2) WILD-TYPE       5        1        1       11        36
                               vv
clus                            STAGE IV
  DEL PEAK 10(8P23.2) MUTATED          4
  DEL PEAK 10(8P23.2) WILD-TYPE        7
D10V3, multiclass
           clus
vv          DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  STAGE I                             2                             5
  STAGE IA                            1                             1
  STAGE IB                            0                             1
  STAGE II                            5                            11
  STAGE III                           4                            36
  STAGE IV                            4                             7
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 10(8P23.2) MUTATED    3  7  2  4
  DEL PEAK 10(8P23.2) WILD-TYPE 11 18 26  4
D10V4, multiclass
    clus
vv   DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  T1                           3                            11
  T2                           7                            18
  T3                           2                            26
  T4                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 10(8P23.2) MUTATED   10  1     5
  DEL PEAK 10(8P23.2) WILD-TYPE 32  9    16
D10V5, multiclass
       clus
vv      DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  N0                             10                            32
  N1                              1                             9
  N2+N3                           5                            16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                               cls
clus                             0  1
  DEL PEAK 10(8P23.2) MUTATED   10  0
  DEL PEAK 10(8P23.2) WILD-TYPE 39  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(8P23.2) MUTATED     10    0
  DEL PEAK 10(8P23.2) WILD-TYPE   39    2
   clus
vv  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  0                          10                            39
  1                           0                             2
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                             0  1
  DEL PEAK 10(8P23.2) MUTATED    2 14
  DEL PEAK 10(8P23.2) WILD-TYPE 13 48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(8P23.2) MUTATED      2   14
  DEL PEAK 10(8P23.2) WILD-TYPE   13   48
        clus
vv       DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  FEMALE                           2                            13
  MALE                            14                            48
[1] 2 2
[1] FALSE
D10V8, continuous

Clustering(11) Variable = DEL PEAK 11(9P21.3) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 11(9P21.3) MUTATED    4 43
  DEL PEAK 11(9P21.3) WILD-TYPE  7 22
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                           47                            29 
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                           43                            22 
$`DEL PEAK 11(9P21.3) MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3S TCGA-3H-AB3T TCGA-LK-A4NW TCGA-LK-A4NY 
       11.87        29.10        12.66        13.61        17.95         5.52 
TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        6.08         1.87        12.72        11.51        18.81        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-NQ-A57I 
        5.19        17.33         3.52        10.95        19.99         0.66 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A9CU 
       28.96        13.61         2.56         9.76        23.90        14.76 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P6 TCGA-TS-A7P7 
        8.38        27.75        41.46        18.51         9.30        19.43 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC4 
       11.77        10.78        15.42        27.72         6.48        23.64 
TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G 
        8.32        14.99        13.35        21.44        14.27         2.50 
TCGA-XT-AASU TCGA-YS-A95B TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VW 
        4.67         1.28        16.41        33.70         2.76 

$`DEL PEAK 11(9P21.3) WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3O TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NZ TCGA-LK-A4O4 
       56.38        42.81        27.16        26.40         8.02        31.20 
TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       14.73        80.84        91.73        24.89        66.54        62.27 
TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU 
       29.42        17.72        15.09         7.99        14.76        55.07 
TCGA-TS-A7P3 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AS TCGA-TS-A8AV TCGA-UD-AAC1 
       22.65        15.02        32.28        26.14         1.55        25.94 
TCGA-UT-A88C TCGA-UT-A97Y TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VU 
       23.77         4.73         4.37         2.76        24.30 

  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                         0.66                          1.55 
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                        41.46                         91.73 
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                        13.35                         24.89 
[1] "0.7 - 41.5 (13.3)" "1.6 - 91.7 (24.9)"
[1] "hr=" "3"  
D11V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 11(9P21.3) MUTATED         5        1        1       10        24
  DEL PEAK 11(9P21.3) WILD-TYPE       2        1        0        6        16
                               vv
clus                            STAGE IV
  DEL PEAK 11(9P21.3) MUTATED          7
  DEL PEAK 11(9P21.3) WILD-TYPE        4
D11V3, multiclass
           clus
vv          DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  STAGE I                             5                             2
  STAGE IA                            1                             1
  STAGE IB                            1                             0
  STAGE II                           10                             6
  STAGE III                          24                            16
  STAGE IV                            7                             4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 11(9P21.3) MUTATED    7 14 20  6
  DEL PEAK 11(9P21.3) WILD-TYPE  7 11  8  2
D11V4, multiclass
    clus
vv   DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  T1                           7                             7
  T2                          14                            11
  T3                          20                             8
  T4                           6                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2+N3
  DEL PEAK 11(9P21.3) MUTATED   26  5    13
  DEL PEAK 11(9P21.3) WILD-TYPE 16  5     8
D11V5, multiclass
       clus
vv      DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  N0                             26                            16
  N1                              5                             5
  N2+N3                          13                             8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                               cls
clus                             0  1
  DEL PEAK 11(9P21.3) MUTATED   32  0
  DEL PEAK 11(9P21.3) WILD-TYPE 17  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(9P21.3) MUTATED     32    0
  DEL PEAK 11(9P21.3) WILD-TYPE   17    2
   clus
vv  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  0                          32                            17
  1                           0                             2
[1] 2 2
[1] FALSE
D11V7, binary
                               cls
clus                             0  1
  DEL PEAK 11(9P21.3) MUTATED    9 39
  DEL PEAK 11(9P21.3) WILD-TYPE  6 23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(9P21.3) MUTATED      9   39
  DEL PEAK 11(9P21.3) WILD-TYPE    6   23
        clus
vv       DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  FEMALE                           9                             6
  MALE                            39                            23
[1] 2 2
[1] FALSE
D11V8, continuous

Clustering(12) Variable = DEL PEAK 12(10P15.3) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 12(10P15.3) MUTATED    2 23
  DEL PEAK 12(10P15.3) WILD-TYPE  9 42
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                            25                             51 
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                            23                             42 
$`DEL PEAK 12(10P15.3) MUTATED`
TCGA-3H-AB3L TCGA-LK-A4NY TCGA-LK-A4O2 TCGA-LK-A4O7 TCGA-MQ-A4LM TCGA-MQ-A4LP 
       11.87         5.52         1.87        11.51         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7P1 
        3.52        19.99         0.66         7.99        14.76        18.51 
TCGA-TS-A7P6 TCGA-TS-A7P8 TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY 
        9.30        15.02        11.77        10.78        15.42        27.72 
TCGA-UD-AAC5 TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-ZN-A9VQ 
        8.32        14.27         2.50         4.73         4.67        16.41 
TCGA-ZN-A9VW 
        2.76 

$`DEL PEAK 12(10P15.3) WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U 
       56.38        29.10        42.81        12.66        13.61        27.16 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O4 TCGA-LK-A4O5 
       26.40        17.95         8.02         6.08        31.20        12.72 
TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BL 
       14.73        80.84        91.73        18.81        23.31        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP 
       24.89        66.54        62.27        28.96        13.61         2.56 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT 
        9.76        29.42        17.72        23.90        15.09        14.76 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P3 TCGA-TS-A7P7 
       55.07         8.38        27.75        41.46        22.65        19.43 
TCGA-TS-A7PB TCGA-TS-A8AS TCGA-TS-A8AV TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 
       32.28        26.14         1.55         6.48        25.94        23.64 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88D TCGA-YS-A95B TCGA-YS-A95C 
       14.99        13.35        23.77        21.44         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VS TCGA-ZN-A9VU 
        2.76        33.70        24.30 

  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                          0.66                           1.28 
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                         27.72                          91.73 
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                         10.78                          22.65 
[1] "0.7 - 27.7 (10.8)" "1.3 - 91.7 (22.6)"
[1] "hr=" "3.4"
D12V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 12(10P15.3) MUTATED         5        0        1        2        15
  DEL PEAK 12(10P15.3) WILD-TYPE       2        2        0       14        25
                                vv
clus                             STAGE IV
  DEL PEAK 12(10P15.3) MUTATED          3
  DEL PEAK 12(10P15.3) WILD-TYPE        8
D12V3, multiclass
           clus
vv          DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE
  STAGE I                              5                              2
  STAGE IA                             0                              2
  STAGE IB                             1                              0
  STAGE II                             2                             14
  STAGE III                           15                             25
  STAGE IV                             3                              8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 12(10P15.3) MUTATED    6  3 12  3
  DEL PEAK 12(10P15.3) WILD-TYPE  8 22 16  5
D12V4, multiclass
    clus
vv   DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE
  T1                            6                              8
  T2                            3                             22
  T3                           12                             16
  T4                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 12(10P15.3) MUTATED   15  4     4
  DEL PEAK 12(10P15.3) WILD-TYPE 27  6    17
D12V5, multiclass
       clus
vv      DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE
  N0                              15                             27
  N1                               4                              6
  N2+N3                            4                             17
[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"
D12V6, binary
                                cls
clus                              0  1
  DEL PEAK 12(10P15.3) MUTATED   14  0
  DEL PEAK 12(10P15.3) WILD-TYPE 35  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(10P15.3) MUTATED     14    0
  DEL PEAK 12(10P15.3) WILD-TYPE   35    2
   clus
vv  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE
  0                           14                             35
  1                            0                              2
[1] 2 2
[1] FALSE
D12V7, binary
                                cls
clus                              0  1
  DEL PEAK 12(10P15.3) MUTATED    5 21
  DEL PEAK 12(10P15.3) WILD-TYPE 10 41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(10P15.3) MUTATED      5   21
  DEL PEAK 12(10P15.3) WILD-TYPE   10   41
        clus
vv       DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE
  FEMALE                            5                             10
  MALE                             21                             41
[1] 2 2
[1] FALSE
D12V8, continuous

Clustering(13) Variable = DEL PEAK 13(10Q25.2) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 13(10Q25.2) MUTATED    2 25
  DEL PEAK 13(10Q25.2) WILD-TYPE  9 40
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                            27                             49 
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                            25                             40 
$`DEL PEAK 13(10Q25.2) MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-LK-A4NY TCGA-LK-A4O7 TCGA-MQ-A4LP TCGA-MQ-A4LV 
       11.87        29.10         5.52        11.51        17.33         3.52 
TCGA-MQ-A6BN TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SH-A7BD TCGA-SH-A7BH 
       24.89        19.99         0.66        28.96        15.09         7.99 
TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7P6 TCGA-TS-A7P8 TCGA-TS-A7PB 
       14.76        14.76        55.07         9.30        15.02        32.28 
TCGA-TS-A8AI TCGA-UD-AABY TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88D TCGA-UT-A88G 
       10.78        27.72         8.32        13.35        21.44         2.50 
TCGA-UT-A97Y TCGA-XT-AASU TCGA-ZN-A9VW 
        4.73         4.67         2.76 

$`DEL PEAK 13(10Q25.2) WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X 
       56.38        42.81        12.66        13.61        27.16        26.40 
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 
       17.95         8.02         6.08         1.87        31.20        12.72 
TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       14.73        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A6BL TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       10.95        66.54        62.27        13.61         2.56         9.76 
TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 
       29.42        17.72        23.90         8.38        27.75        41.46 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A8AF TCGA-TS-A8AS TCGA-TS-A8AV 
       18.51        22.65        19.43        11.77        26.14         1.55 
TCGA-TS-A8AY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C 
       15.42         6.48        25.94        23.64        14.99        23.77 
TCGA-UT-A88E TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS 
       14.27         1.28         4.37         2.76        16.41        33.70 
TCGA-ZN-A9VU 
       24.30 

  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                          0.66                           1.28 
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                         55.07                          91.73 
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                         13.35                          17.95 
[1] "0.7 - 55.1 (13.3)" "1.3 - 91.7 (17.9)"
[1] "hr=" "1.7"
D13V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 13(10Q25.2) MUTATED         2        0        1        5        14
  DEL PEAK 13(10Q25.2) WILD-TYPE       5        2        0       11        26
                                vv
clus                             STAGE IV
  DEL PEAK 13(10Q25.2) MUTATED          6
  DEL PEAK 13(10Q25.2) WILD-TYPE        5
D13V3, multiclass
           clus
vv          DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  STAGE I                              2                              5
  STAGE IA                             0                              2
  STAGE IB                             1                              0
  STAGE II                             5                             11
  STAGE III                           14                             26
  STAGE IV                             6                              5
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 13(10Q25.2) MUTATED    3  7 11  5
  DEL PEAK 13(10Q25.2) WILD-TYPE 11 18 17  3
D13V4, multiclass
    clus
vv   DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  T1                            3                             11
  T2                            7                             18
  T3                           11                             17
  T4                            5                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 13(10Q25.2) MUTATED   15  4     5
  DEL PEAK 13(10Q25.2) WILD-TYPE 27  6    16
D13V5, multiclass
       clus
vv      DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  N0                              15                             27
  N1                               4                              6
  N2+N3                            5                             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                                cls
clus                              0  1
  DEL PEAK 13(10Q25.2) MUTATED   16  1
  DEL PEAK 13(10Q25.2) WILD-TYPE 33  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q25.2) MUTATED     16    1
  DEL PEAK 13(10Q25.2) WILD-TYPE   33    1
   clus
vv  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  0                           16                             33
  1                            1                              1
[1] 2 2
[1] FALSE
D13V7, binary
                                cls
clus                              0  1
  DEL PEAK 13(10Q25.2) MUTATED    6 22
  DEL PEAK 13(10Q25.2) WILD-TYPE  9 40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q25.2) MUTATED      6   22
  DEL PEAK 13(10Q25.2) WILD-TYPE    9   40
        clus
vv       DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  FEMALE                            6                              9
  MALE                             22                             40
[1] 2 2
[1] FALSE
D13V8, continuous
[1] "Remove cluster labels:"       "DEL PEAK 13(10Q25.2) MUTATED"
clus
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                             2                              4 
                    TCGA-SC-A6LR                     TCGA-ZN-A9VQ 
"DEL PEAK 13(10Q25.2) WILD-TYPE" "DEL PEAK 13(10Q25.2) WILD-TYPE" 
                    TCGA-ZN-A9VS                     TCGA-ZN-A9VU 
"DEL PEAK 13(10Q25.2) WILD-TYPE" "DEL PEAK 13(10Q25.2) WILD-TYPE" 

Clustering(14) Variable = DEL PEAK 14(11Q23.2) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 14(11Q23.2) MUTATED    1 14
  DEL PEAK 14(11Q23.2) WILD-TYPE 10 51
  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE 
                            15                             61 
  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE 
                            14                             51 
$`DEL PEAK 14(11Q23.2) MUTATED`
TCGA-3H-AB3M TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4O0 
       29.10        12.66        13.61        26.40        17.95         6.08 
TCGA-LK-A4O7 TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-NQ-A57I TCGA-SC-A6LQ TCGA-SH-A9CT 
       11.51         5.19         3.52         0.66         9.76        14.76 
TCGA-TS-A7OZ TCGA-UD-AABY TCGA-UD-AABZ 
       27.75        27.72         6.48 

$`DEL PEAK 14(11Q23.2) WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3U TCGA-LK-A4NY TCGA-LK-A4NZ 
       56.38        11.87        42.81        27.16         5.52         8.02 
TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        1.87        31.20        12.72        14.73        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       18.81        23.31        17.33        10.95        24.89        66.54 
TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LR 
       62.27        19.99        28.96        13.61         2.56        29.42 
TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7OU 
       17.72        23.90        15.09         7.99        14.76        55.07 
TCGA-TS-A7OY TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 
        8.38        41.46        18.51        22.65         9.30        19.43 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV 
       15.02        32.28        11.77        10.78        26.14         1.55 
TCGA-TS-A8AY TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
       15.42        25.94        23.64         8.32        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU 
       23.77        21.44        14.27         2.50         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        1.28         4.37         2.76        16.41        33.70        24.30 
TCGA-ZN-A9VW 
        2.76 

  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE 
                          0.66                           1.28 
  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE 
                         29.10                          91.73 
  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE 
                         12.66                          16.41 
[1] "0.7 - 29.1 (12.7)" "1.3 - 91.7 (16.4)"
[1] "hr=" "1.7"
D14V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 14(11Q23.2) MUTATED         1        1        1        4         8
  DEL PEAK 14(11Q23.2) WILD-TYPE       6        1        0       12        32
                                vv
clus                             STAGE IV
  DEL PEAK 14(11Q23.2) MUTATED          1
  DEL PEAK 14(11Q23.2) WILD-TYPE       10
D14V3, multiclass
           clus
vv          DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE
  STAGE I                              1                              6
  STAGE IA                             1                              1
  STAGE IB                             1                              0
  STAGE II                             4                             12
  STAGE III                            8                             32
  STAGE IV                             1                             10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 14(11Q23.2) MUTATED    3  4  8  1
  DEL PEAK 14(11Q23.2) WILD-TYPE 11 21 20  7
D14V4, multiclass
    clus
vv   DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE
  T1                            3                             11
  T2                            4                             21
  T3                            8                             20
  T4                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 14(11Q23.2) MUTATED    9  2     3
  DEL PEAK 14(11Q23.2) WILD-TYPE 33  8    18
D14V5, multiclass
       clus
vv      DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE
  N0                               9                             33
  N1                               2                              8
  N2+N3                            3                             18
[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"
D14V6, binary
                                cls
clus                              0  1
  DEL PEAK 14(11Q23.2) MUTATED   13  0
  DEL PEAK 14(11Q23.2) WILD-TYPE 36  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q23.2) MUTATED     13    0
  DEL PEAK 14(11Q23.2) WILD-TYPE   36    2
   clus
vv  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE
  0                           13                             36
  1                            0                              2
[1] 2 2
[1] FALSE
D14V7, binary
                                cls
clus                              0  1
  DEL PEAK 14(11Q23.2) MUTATED    2 14
  DEL PEAK 14(11Q23.2) WILD-TYPE 13 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q23.2) MUTATED      2   14
  DEL PEAK 14(11Q23.2) WILD-TYPE   13   48
        clus
vv       DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE
  FEMALE                            2                             13
  MALE                             14                             48
[1] 2 2
[1] FALSE
D14V8, continuous

Clustering(15) Variable = DEL PEAK 15(12P13.31) MUTATION ANALYSIS
D15V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 15(12P13.31) MUTATED    0  9
  DEL PEAK 15(12P13.31) WILD-TYPE 11 56
  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE 
                              9                              67 
  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE 
                              9                              56 
$`DEL PEAK 15(12P13.31) MUTATED`
TCGA-3H-AB3T TCGA-LK-A4O7 TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CT 
       13.61        11.51         0.66        23.90         7.99        14.76 
TCGA-TS-A7P0 TCGA-UD-AAC7 TCGA-ZN-A9VW 
       41.46        13.35         2.76 

$`DEL PEAK 15(12P13.31) WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3U 
       56.38        11.87        29.10        42.81        12.66        27.16 
TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 
       26.40        17.95         5.52         8.02         6.08         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       31.20        12.72        14.73        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       23.31         5.19        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP 
       66.54        62.27        19.99        28.96        13.61         2.56 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BD TCGA-SH-A9CU TCGA-TS-A7OU 
        9.76        29.42        17.72        15.09        14.76        55.07 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 
        8.38        27.75        18.51        22.65         9.30        19.43 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV 
       15.02        32.28        11.77        10.78        26.14         1.55 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 
       15.42        27.72         6.48        25.94        23.64         8.32 
TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
       14.99        23.77        21.44        14.27         2.50         4.73 
TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.67         1.28         4.37         2.76        16.41        33.70 
TCGA-ZN-A9VU 
       24.30 

  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE 
                           0.66                            1.28 
  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE 
                          41.46                           91.73 
  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE 
                          13.35                           16.41 
[1] "0.7 - 41.5 (13.3)" "1.3 - 91.7 (16.4)"
[1] "hr=" "1.8"
D15V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 15(12P13.31) MUTATED         1        0        1        2         4
  DEL PEAK 15(12P13.31) WILD-TYPE       6        2        0       14        36
                                 vv
clus                              STAGE IV
  DEL PEAK 15(12P13.31) MUTATED          1
  DEL PEAK 15(12P13.31) WILD-TYPE       10
D15V3, multiclass
           clus
vv          DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE
  STAGE I                               1                               6
  STAGE IA                              0                               2
  STAGE IB                              1                               0
  STAGE II                              2                              14
  STAGE III                             4                              36
  STAGE IV                              1                              10
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T1 T2 T3 T4
  DEL PEAK 15(12P13.31) MUTATED    2  2  4  1
  DEL PEAK 15(12P13.31) WILD-TYPE 12 23 24  7
D15V4, multiclass
    clus
vv   DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE
  T1                             2                              12
  T2                             2                              23
  T3                             4                              24
  T4                             1                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2+N3
  DEL PEAK 15(12P13.31) MUTATED    6  1     1
  DEL PEAK 15(12P13.31) WILD-TYPE 36  9    20
D15V5, multiclass
       clus
vv      DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE
  N0                                6                              36
  N1                                1                               9
  N2+N3                             1                              20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                                 cls
clus                               0  1
  DEL PEAK 15(12P13.31) MUTATED    6  0
  DEL PEAK 15(12P13.31) WILD-TYPE 43  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(12P13.31) MUTATED      6    0
  DEL PEAK 15(12P13.31) WILD-TYPE   43    2
   clus
vv  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE
  0                             6                              43
  1                             0                               2
[1] 2 2
[1] FALSE
D15V7, binary
                                 cls
clus                               0  1
  DEL PEAK 15(12P13.31) MUTATED    1  8
  DEL PEAK 15(12P13.31) WILD-TYPE 14 54
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(12P13.31) MUTATED      1    8
  DEL PEAK 15(12P13.31) WILD-TYPE   14   54
        clus
vv       DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE
  FEMALE                             1                              14
  MALE                               8                              54
[1] 2 2
[1] FALSE
D15V8, continuous
[1] "Remove cluster labels:"        "DEL PEAK 15(12P13.31) MUTATED"
clus
  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE 
                              1                               5 
                     TCGA-SC-A6LR                      TCGA-XT-AASU 
"DEL PEAK 15(12P13.31) WILD-TYPE" "DEL PEAK 15(12P13.31) WILD-TYPE" 
                     TCGA-ZN-A9VQ                      TCGA-ZN-A9VS 
"DEL PEAK 15(12P13.31) WILD-TYPE" "DEL PEAK 15(12P13.31) WILD-TYPE" 
                     TCGA-ZN-A9VU 
"DEL PEAK 15(12P13.31) WILD-TYPE" 

Clustering(16) Variable = DEL PEAK 16(13Q14.11) MUTATION ANALYSIS
D16V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 16(13Q14.11) MUTATED    5 36
  DEL PEAK 16(13Q14.11) WILD-TYPE  6 29
  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE 
                             41                              35 
  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE 
                             36                              29 
$`DEL PEAK 16(13Q14.11) MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3S TCGA-3H-AB3T TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O2 
       11.87        12.66        13.61        17.95         6.08         1.87 
TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       12.72        80.84        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SH-A7BC 
        3.52        10.95        19.99        13.61         2.56        23.90 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OY TCGA-TS-A7P0 
       15.09         7.99        14.76        14.76         8.38        41.46 
TCGA-TS-A7P1 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS 
       18.51         9.30        19.43        11.77        10.78        26.14 
TCGA-TS-A8AY TCGA-UD-AABZ TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G 
       15.42         6.48        13.35        23.77        14.27         2.50 
TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        2.76        16.41        33.70        24.30         2.76 

$`DEL PEAK 16(13Q14.11) WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NY 
       56.38        29.10        42.81        27.16        26.40         5.52 
TCGA-LK-A4NZ TCGA-LK-A4O4 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LP TCGA-MQ-A6BN 
        8.02        31.20        14.73        11.51        17.33        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LQ TCGA-SC-A6LR 
       66.54        62.27         0.66        28.96         9.76        29.42 
TCGA-SC-AA5Z TCGA-TS-A7OU TCGA-TS-A7OZ TCGA-TS-A7P3 TCGA-TS-A7P8 TCGA-TS-A7PB 
       17.72        55.07        27.75        22.65        15.02        32.28 
TCGA-TS-A8AV TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 
        1.55        27.72        25.94        23.64         8.32        14.99 
TCGA-UT-A88D TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       21.44         4.73         4.67         1.28         4.37 

  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE 
                           1.87                            0.66 
  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE 
                          91.73                           66.54 
  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE 
                          13.61                           22.65 
[1] "1.9 - 91.7 (13.6)" "0.7 - 66.5 (22.6)"
[1] "hr=" "1.5"
D16V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 16(13Q14.11) MUTATED         5        2        0       10        17
  DEL PEAK 16(13Q14.11) WILD-TYPE       2        0        1        6        23
                                 vv
clus                              STAGE IV
  DEL PEAK 16(13Q14.11) MUTATED          7
  DEL PEAK 16(13Q14.11) WILD-TYPE        4
D16V3, multiclass
           clus
vv          DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE
  STAGE I                               5                               2
  STAGE IA                              2                               0
  STAGE IB                              0                               1
  STAGE II                             10                               6
  STAGE III                            17                              23
  STAGE IV                              7                               4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T1 T2 T3 T4
  DEL PEAK 16(13Q14.11) MUTATED    8 14 14  4
  DEL PEAK 16(13Q14.11) WILD-TYPE  6 11 14  4
D16V4, multiclass
    clus
vv   DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE
  T1                             8                               6
  T2                            14                              11
  T3                            14                              14
  T4                             4                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2+N3
  DEL PEAK 16(13Q14.11) MUTATED   28  3    10
  DEL PEAK 16(13Q14.11) WILD-TYPE 14  7    11
D16V5, multiclass
       clus
vv      DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE
  N0                               28                              14
  N1                                3                               7
  N2+N3                            10                              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                                 cls
clus                               0  1
  DEL PEAK 16(13Q14.11) MUTATED   25  2
  DEL PEAK 16(13Q14.11) WILD-TYPE 24  0
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(13Q14.11) MUTATED     25    2
  DEL PEAK 16(13Q14.11) WILD-TYPE   24    0
   clus
vv  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE
  0                            25                              24
  1                             2                               0
[1] 2 2
[1] FALSE
D16V7, binary
                                 cls
clus                               0  1
  DEL PEAK 16(13Q14.11) MUTATED    5 36
  DEL PEAK 16(13Q14.11) WILD-TYPE 10 26
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(13Q14.11) MUTATED      5   36
  DEL PEAK 16(13Q14.11) WILD-TYPE   10   26
        clus
vv       DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE
  FEMALE                             5                              10
  MALE                              36                              26
[1] 2 2
[1] FALSE
D16V8, continuous
[1] "Remove cluster labels:"          "DEL PEAK 16(13Q14.11) WILD-TYPE"
clus
  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE 
                              4                               2 
                   TCGA-SH-A7BH                    TCGA-ZN-A9VQ 
"DEL PEAK 16(13Q14.11) MUTATED" "DEL PEAK 16(13Q14.11) MUTATED" 
                   TCGA-ZN-A9VS                    TCGA-ZN-A9VU 
"DEL PEAK 16(13Q14.11) MUTATED" "DEL PEAK 16(13Q14.11) MUTATED" 

Clustering(17) Variable = DEL PEAK 17(14Q32.31) MUTATION ANALYSIS
D17V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 17(14Q32.31) MUTATED    4 31
  DEL PEAK 17(14Q32.31) WILD-TYPE  7 34
  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE 
                             35                              41 
  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE 
                             31                              34 
$`DEL PEAK 17(14Q32.31) MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3S TCGA-3H-AB3X TCGA-LK-A4NY TCGA-LK-A4O0 
       11.87        29.10        12.66        26.40         5.52         6.08 
TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ 
        1.87        12.72        14.73        11.51        18.81        23.31 
TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A7BH 
       66.54        19.99        13.61         9.76        23.90         7.99 
TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P6 
       14.76        14.76         8.38        27.75        41.46         9.30 
TCGA-TS-A7P8 TCGA-TS-A8AF TCGA-TS-A8AY TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UD-AAC7 
       15.02        11.77        15.42         6.48         8.32        13.35 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-YS-A95B TCGA-ZN-A9VS 
       14.27         2.50         4.73         1.28        33.70 

$`DEL PEAK 17(14Q32.31) WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3O TCGA-3H-AB3T TCGA-3H-AB3U TCGA-LK-A4NW TCGA-LK-A4NZ 
       56.38        42.81        13.61        27.16        17.95         8.02 
TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV 
       31.20        80.84        91.73         5.19        17.33         3.52 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP 
       10.95        24.89        62.27         0.66        28.96         2.56 
TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BD TCGA-TS-A7OU TCGA-TS-A7P1 TCGA-TS-A7P3 
       29.42        17.72        15.09        55.07        18.51        22.65 
TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-UD-AABY 
       19.43        32.28        10.78        26.14         1.55        27.72 
TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88D TCGA-XT-AASU 
       25.94        23.64        14.99        23.77        21.44         4.67 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VU TCGA-ZN-A9VW 
        4.37         2.76        16.41        24.30         2.76 

  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE 
                           1.28                            0.66 
  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE 
                          66.54                           91.73 
  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE 
                          13.35                           19.43 
[1] "1.3 - 66.5 (13.3)" "0.7 - 91.7 (19.4)"
[1] "hr=" "1.7"
D17V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 17(14Q32.31) MUTATED         3        1        0        8        21
  DEL PEAK 17(14Q32.31) WILD-TYPE       4        1        1        8        19
                                 vv
clus                              STAGE IV
  DEL PEAK 17(14Q32.31) MUTATED          3
  DEL PEAK 17(14Q32.31) WILD-TYPE        8
D17V3, multiclass
           clus
vv          DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE
  STAGE I                               3                               4
  STAGE IA                              1                               1
  STAGE IB                              0                               1
  STAGE II                              8                               8
  STAGE III                            21                              19
  STAGE IV                              3                               8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T1 T2 T3 T4
  DEL PEAK 17(14Q32.31) MUTATED    4 11 17  2
  DEL PEAK 17(14Q32.31) WILD-TYPE 10 14 11  6
D17V4, multiclass
    clus
vv   DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE
  T1                             4                              10
  T2                            11                              14
  T3                            17                              11
  T4                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2+N3
  DEL PEAK 17(14Q32.31) MUTATED   19  6    10
  DEL PEAK 17(14Q32.31) WILD-TYPE 23  4    11
D17V5, multiclass
       clus
vv      DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE
  N0                               19                              23
  N1                                6                               4
  N2+N3                            10                              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                                 cls
clus                               0  1
  DEL PEAK 17(14Q32.31) MUTATED   25  0
  DEL PEAK 17(14Q32.31) WILD-TYPE 24  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(14Q32.31) MUTATED     25    0
  DEL PEAK 17(14Q32.31) WILD-TYPE   24    2
   clus
vv  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE
  0                            25                              24
  1                             0                               2
[1] 2 2
[1] FALSE
D17V7, binary
                                 cls
clus                               0  1
  DEL PEAK 17(14Q32.31) MUTATED   11 25
  DEL PEAK 17(14Q32.31) WILD-TYPE  4 37
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(14Q32.31) MUTATED     11   25
  DEL PEAK 17(14Q32.31) WILD-TYPE    4   37
        clus
vv       DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE
  FEMALE                            11                               4
  MALE                              25                              37
[1] 2 2
[1] FALSE
D17V8, continuous
[1] "Remove cluster labels:"        "DEL PEAK 17(14Q32.31) MUTATED"
clus
  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE 
                              2                               4 
                     TCGA-SC-A6LR                      TCGA-XT-AASU 
"DEL PEAK 17(14Q32.31) WILD-TYPE" "DEL PEAK 17(14Q32.31) WILD-TYPE" 
                     TCGA-ZN-A9VQ                      TCGA-ZN-A9VU 
"DEL PEAK 17(14Q32.31) WILD-TYPE" "DEL PEAK 17(14Q32.31) WILD-TYPE" 

Clustering(18) Variable = DEL PEAK 18(15Q15.1) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(15Q15.1) MUTATED    1 23
  DEL PEAK 18(15Q15.1) WILD-TYPE 10 42
  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE 
                            24                             52 
  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE 
                            23                             42 
$`DEL PEAK 18(15Q15.1) MUTATED`
TCGA-3H-AB3M TCGA-3H-AB3S TCGA-3H-AB3T TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-MQ-A4LJ 
       29.10        12.66        13.61         5.52         6.08        23.31 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LN 
       17.33         3.52        24.89        19.99         0.66        13.61 
TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-TS-A7P6 
       23.90         7.99        14.76        14.76        41.46         9.30 
TCGA-TS-A8AF TCGA-UD-AABY TCGA-UD-AABZ TCGA-XT-AASU TCGA-YS-A95B TCGA-ZN-A9VW 
       11.77        27.72         6.48         4.67         1.28         2.76 

$`DEL PEAK 18(15Q15.1) WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3O TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW 
       56.38        11.87        42.81        27.16        26.40        17.95 
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 
        8.02         1.87        31.20        12.72        14.73        11.51 
TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BQ 
       80.84        91.73        18.81         5.19        10.95        66.54 
TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z 
       62.27        28.96         2.56         9.76        29.42        17.72 
TCGA-SH-A7BD TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 
       15.09        55.07         8.38        27.75        18.51        22.65 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV 
       19.43        15.02        32.28        10.78        26.14         1.55 
TCGA-TS-A8AY TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
       15.42        25.94        23.64         8.32        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-YS-A95C 
       23.77        21.44        14.27         2.50         4.73         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        2.76        16.41        33.70        24.30 

  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE 
                          0.66                           1.55 
  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE 
                         41.46                          91.73 
  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE 
                        13.135                         17.835 
[1] "0.7 - 41.5 (13.1)" "1.6 - 91.7 (17.8)"
[1] "hr=" "2"  
D18V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 18(15Q15.1) MUTATED         1        1        1        5        14
  DEL PEAK 18(15Q15.1) WILD-TYPE       6        1        0       11        26
                                vv
clus                             STAGE IV
  DEL PEAK 18(15Q15.1) MUTATED          3
  DEL PEAK 18(15Q15.1) WILD-TYPE        8
D18V3, multiclass
           clus
vv          DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE
  STAGE I                              1                              6
  STAGE IA                             1                              1
  STAGE IB                             1                              0
  STAGE II                             5                             11
  STAGE III                           14                             26
  STAGE IV                             3                              8
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 18(15Q15.1) MUTATED    3  9 10  3
  DEL PEAK 18(15Q15.1) WILD-TYPE 11 16 18  5
D18V4, multiclass
    clus
vv   DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE
  T1                            3                             11
  T2                            9                             16
  T3                           10                             18
  T4                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 18(15Q15.1) MUTATED   13  2     7
  DEL PEAK 18(15Q15.1) WILD-TYPE 29  8    14
D18V5, multiclass
       clus
vv      DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE
  N0                              13                             29
  N1                               2                              8
  N2+N3                            7                             14
[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"
D18V6, binary
                                cls
clus                              0  1
  DEL PEAK 18(15Q15.1) MUTATED   16  0
  DEL PEAK 18(15Q15.1) WILD-TYPE 33  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(15Q15.1) MUTATED     16    0
  DEL PEAK 18(15Q15.1) WILD-TYPE   33    2
   clus
vv  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE
  0                           16                             33
  1                            0                              2
[1] 2 2
[1] FALSE
D18V7, binary
                                cls
clus                              0  1
  DEL PEAK 18(15Q15.1) MUTATED    5 20
  DEL PEAK 18(15Q15.1) WILD-TYPE 10 42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(15Q15.1) MUTATED      5   20
  DEL PEAK 18(15Q15.1) WILD-TYPE   10   42
        clus
vv       DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE
  FEMALE                            5                             10
  MALE                             20                             42
[1] 2 2
[1] FALSE
D18V8, continuous
[1] "Remove cluster labels:"       "DEL PEAK 18(15Q15.1) MUTATED"
clus
  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE 
                             2                              4 
                    TCGA-SC-A6LR                     TCGA-ZN-A9VQ 
"DEL PEAK 18(15Q15.1) WILD-TYPE" "DEL PEAK 18(15Q15.1) WILD-TYPE" 
                    TCGA-ZN-A9VS                     TCGA-ZN-A9VU 
"DEL PEAK 18(15Q15.1) WILD-TYPE" "DEL PEAK 18(15Q15.1) WILD-TYPE" 

Clustering(19) Variable = DEL PEAK 19(16P13.3) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 19(16P13.3) MUTATED    1  4
  DEL PEAK 19(16P13.3) WILD-TYPE 10 61
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                             5                             71 
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                             4                             61 
$`DEL PEAK 19(16P13.3) MUTATED`
TCGA-LK-A4O0 TCGA-MQ-A4LM TCGA-MQ-A6BR TCGA-UT-A88G TCGA-UT-A97Y 
        6.08         5.19        62.27         2.50         4.73 

$`DEL PEAK 19(16P13.3) WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3T 
       56.38        11.87        29.10        42.81        12.66        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 
       27.16        26.40        17.95         5.52         8.02         1.87 
TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC 
       31.20        12.72        14.73        11.51        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       18.81        23.31        17.33         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP 
       66.54        19.99         0.66        28.96        13.61         2.56 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
        9.76        29.42        17.72        23.90        15.09         7.99 
TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 
       14.76        14.76        55.07         8.38        27.75        41.46 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB 
       18.51        22.65         9.30        19.43        15.02        32.28 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AABY 
       11.77        10.78        26.14         1.55        15.42        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
        6.48        25.94        23.64         8.32        14.99        13.35 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       23.77        21.44        14.27         4.67         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        2.76        16.41        33.70        24.30         2.76 

  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                          2.50                           0.66 
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                         62.27                          91.73 
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                          5.19                          15.42 
[1] "2.5 - 62.3 (5.2)"  "0.7 - 91.7 (15.4)"
[1] "hr=" "1.4"
D19V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 19(16P13.3) MUTATED         1        1        0        0         3
  DEL PEAK 19(16P13.3) WILD-TYPE       6        1        1       16        37
                                vv
clus                             STAGE IV
  DEL PEAK 19(16P13.3) MUTATED          0
  DEL PEAK 19(16P13.3) WILD-TYPE       11
D19V3, multiclass
           clus
vv          DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  STAGE I                              1                              6
  STAGE IA                             1                              1
  STAGE IB                             0                              1
  STAGE II                             0                             16
  STAGE III                            3                             37
  STAGE IV                             0                             11
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 19(16P13.3) MUTATED    3  0  2  0
  DEL PEAK 19(16P13.3) WILD-TYPE 11 25 26  8
D19V4, multiclass
    clus
vv   DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  T1                            3                             11
  T2                            0                             25
  T3                            2                             26
  T4                            0                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 19(16P13.3) MUTATED    4  1     0
  DEL PEAK 19(16P13.3) WILD-TYPE 38  9    21
D19V5, multiclass
       clus
vv      DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  N0                               4                             38
  N1                               1                              9
  N2+N3                            0                             21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                                cls
clus                              0  1
  DEL PEAK 19(16P13.3) MUTATED    4  0
  DEL PEAK 19(16P13.3) WILD-TYPE 45  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(16P13.3) MUTATED      4    0
  DEL PEAK 19(16P13.3) WILD-TYPE   45    2
   clus
vv  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  0                            4                             45
  1                            0                              2
[1] 2 2
[1] FALSE
D19V7, binary
                                cls
clus                              0  1
  DEL PEAK 19(16P13.3) MUTATED    2  3
  DEL PEAK 19(16P13.3) WILD-TYPE 13 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(16P13.3) MUTATED      2    3
  DEL PEAK 19(16P13.3) WILD-TYPE   13   59
        clus
vv       DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  FEMALE                            2                             13
  MALE                              3                             59
[1] 2 2
[1] FALSE
D19V8, continuous

Clustering(20) Variable = DEL PEAK 20(16Q24.1) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 20(16Q24.1) MUTATED    2 17
  DEL PEAK 20(16Q24.1) WILD-TYPE  9 48
  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE 
                            19                             57 
  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE 
                            17                             48 
$`DEL PEAK 20(16Q24.1) MUTATED`
TCGA-3H-AB3T TCGA-3H-AB3X TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-LK-A4O6 
       13.61        26.40        17.95         5.52         6.08        14.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-SC-A6LQ 
       18.81        23.31        17.33         3.52        19.99         9.76 
TCGA-TS-A8AY TCGA-UD-AABZ TCGA-UD-AAC7 TCGA-UT-A88G TCGA-UT-A97Y TCGA-YS-A95B 
       15.42         6.48        13.35         2.50         4.73         1.28 
TCGA-ZN-A9VQ 
       16.41 

$`DEL PEAK 20(16Q24.1) WILD-TYPE`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3H-AB3U 
       56.38        11.87        29.10        42.81        12.66        27.16 
TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O4 TCGA-LK-A4O5 TCGA-LK-A4O7 TCGA-MQ-A4KX 
        8.02         1.87        31.20        12.72        11.51        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       91.73         5.19        10.95        24.89        66.54        62.27 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SC-AA5Z 
        0.66        28.96        13.61         2.56        29.42        17.72 
TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU 
       23.90        15.09         7.99        14.76        14.76        55.07 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
        8.38        27.75        41.46        18.51        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AS 
       19.43        15.02        32.28        11.77        10.78        26.14 
TCGA-TS-A8AV TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 
        1.55        27.72        25.94        23.64         8.32        14.99 
TCGA-UT-A88C TCGA-UT-A88D TCGA-UT-A88E TCGA-XT-AASU TCGA-YS-A95C TCGA-YS-AA4M 
       23.77        21.44        14.27         4.67         4.37         2.76 
TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
       33.70        24.30         2.76 

  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE 
                          1.28                           0.66 
  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE 
                         26.40                          91.73 
  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE 
                         13.61                          17.72 
[1] "1.3 - 26.4 (13.6)" "0.7 - 91.7 (17.7)"
[1] "hr=" "2.1"
D20V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 20(16Q24.1) MUTATED         3        1        0        5         9
  DEL PEAK 20(16Q24.1) WILD-TYPE       4        1        1       11        31
                                vv
clus                             STAGE IV
  DEL PEAK 20(16Q24.1) MUTATED          2
  DEL PEAK 20(16Q24.1) WILD-TYPE        9
D20V3, multiclass
           clus
vv          DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE
  STAGE I                              3                              4
  STAGE IA                             1                              1
  STAGE IB                             0                              1
  STAGE II                             5                             11
  STAGE III                            9                             31
  STAGE IV                             2                              9
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 20(16Q24.1) MUTATED    4  6  8  2
  DEL PEAK 20(16Q24.1) WILD-TYPE 10 19 20  6
D20V4, multiclass
    clus
vv   DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE
  T1                            4                             10
  T2                            6                             19
  T3                            8                             20
  T4                            2                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 20(16Q24.1) MUTATED   13  3     3
  DEL PEAK 20(16Q24.1) WILD-TYPE 29  7    18
D20V5, multiclass
       clus
vv      DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE
  N0                              13                             29
  N1                               3                              7
  N2+N3                            3                             18
[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"
D20V6, binary
                                cls
clus                              0  1
  DEL PEAK 20(16Q24.1) MUTATED   16  0
  DEL PEAK 20(16Q24.1) WILD-TYPE 33  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(16Q24.1) MUTATED     16    0
  DEL PEAK 20(16Q24.1) WILD-TYPE   33    2
   clus
vv  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE
  0                           16                             33
  1                            0                              2
[1] 2 2
[1] FALSE
D20V7, binary
                                cls
clus                              0  1
  DEL PEAK 20(16Q24.1) MUTATED    7 13
  DEL PEAK 20(16Q24.1) WILD-TYPE  8 49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(16Q24.1) MUTATED      7   13
  DEL PEAK 20(16Q24.1) WILD-TYPE    8   49
        clus
vv       DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE
  FEMALE                            7                              8
  MALE                             13                             49
[1] 2 2
[1] FALSE
D20V8, continuous
[1] "Remove cluster labels:"       "DEL PEAK 20(16Q24.1) MUTATED"
clus
  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE 
                             1                              5 
                    TCGA-SC-A6LR                     TCGA-SH-A7BH 
"DEL PEAK 20(16Q24.1) WILD-TYPE" "DEL PEAK 20(16Q24.1) WILD-TYPE" 
                    TCGA-XT-AASU                     TCGA-ZN-A9VS 
"DEL PEAK 20(16Q24.1) WILD-TYPE" "DEL PEAK 20(16Q24.1) WILD-TYPE" 
                    TCGA-ZN-A9VU 
"DEL PEAK 20(16Q24.1) WILD-TYPE" 

Clustering(21) Variable = DEL PEAK 21(22Q12.2) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 21(22Q12.2) MUTATED    8 51
  DEL PEAK 21(22Q12.2) WILD-TYPE  3 14
  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE 
                            59                             17 
  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE 
                            51                             14 
$`DEL PEAK 21(22Q12.2) MUTATED`
TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3S TCGA-3H-AB3T TCGA-3H-AB3X 
       56.38        11.87        29.10        12.66        13.61        26.40 
TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
        5.52         8.02         6.08         1.87        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
       11.51        91.73        18.81        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM 
        3.52        24.89        66.54        19.99         0.66        28.96 
TCGA-SC-A6LN TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT TCGA-SH-A9CU 
       13.61         9.76        23.90        15.09        14.76        14.76 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 
        8.38        27.75        41.46        18.51        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-UD-AABY 
       19.43        15.02        32.28        11.77        10.78        27.72 
TCGA-UD-AABZ TCGA-UD-AAC4 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
        6.48        23.64         8.32        14.99        13.35        23.77 
TCGA-UT-A88D TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       21.44        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VW 
        4.37        16.41        33.70        24.30         2.76 

$`DEL PEAK 21(22Q12.2) WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3U TCGA-LK-A4NW TCGA-LK-A4O4 TCGA-MQ-A4KX TCGA-MQ-A6BL 
       42.81        27.16        17.95        31.20        80.84        10.95 
TCGA-MQ-A6BR TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SC-AA5Z TCGA-SH-A7BH TCGA-TS-A7OU 
       62.27         2.56        29.42        17.72         7.99        55.07 
TCGA-TS-A8AS TCGA-TS-A8AV TCGA-TS-A8AY TCGA-UD-AAC1 TCGA-YS-AA4M 
       26.14         1.55        15.42        25.94         2.76 

  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE 
                          0.66                           1.55 
  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE 
                         91.73                          80.84 
  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE 
                         14.76                          25.94 
[1] "0.7 - 91.7 (14.8)" "1.6 - 80.8 (25.9)"
[1] "hr=" "1.6"
D21V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 21(22Q12.2) MUTATED         6        1        1       14        31
  DEL PEAK 21(22Q12.2) WILD-TYPE       1        1        0        2         9
                                vv
clus                             STAGE IV
  DEL PEAK 21(22Q12.2) MUTATED          7
  DEL PEAK 21(22Q12.2) WILD-TYPE        4
D21V3, multiclass
           clus
vv          DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE
  STAGE I                              6                              1
  STAGE IA                             1                              1
  STAGE IB                             1                              0
  STAGE II                            14                              2
  STAGE III                           31                              9
  STAGE IV                             7                              4
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 21(22Q12.2) MUTATED    9 20 24  5
  DEL PEAK 21(22Q12.2) WILD-TYPE  5  5  4  3
D21V4, multiclass
    clus
vv   DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE
  T1                            9                              5
  T2                           20                              5
  T3                           24                              4
  T4                            5                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2+N3
  DEL PEAK 21(22Q12.2) MUTATED   33  7    16
  DEL PEAK 21(22Q12.2) WILD-TYPE  9  3     5
D21V5, multiclass
       clus
vv      DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE
  N0                              33                              9
  N1                               7                              3
  N2+N3                           16                              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"
D21V6, binary
                                cls
clus                              0  1
  DEL PEAK 21(22Q12.2) MUTATED   38  1
  DEL PEAK 21(22Q12.2) WILD-TYPE 11  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(22Q12.2) MUTATED     38    1
  DEL PEAK 21(22Q12.2) WILD-TYPE   11    1
   clus
vv  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE
  0                           38                             11
  1                            1                              1
[1] 2 2
[1] FALSE
D21V7, binary
                                cls
clus                              0  1
  DEL PEAK 21(22Q12.2) MUTATED   11 49
  DEL PEAK 21(22Q12.2) WILD-TYPE  4 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(22Q12.2) MUTATED     11   49
  DEL PEAK 21(22Q12.2) WILD-TYPE    4   13
        clus
vv       DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE
  FEMALE                           11                              4
  MALE                             49                             13
[1] 2 2
[1] FALSE
D21V8, continuous
[1] "Remove cluster labels:"         "DEL PEAK 21(22Q12.2) WILD-TYPE"
clus
  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE 
                             4                              2 
                  TCGA-XT-AASU                   TCGA-ZN-A9VQ 
"DEL PEAK 21(22Q12.2) MUTATED" "DEL PEAK 21(22Q12.2) MUTATED" 
                  TCGA-ZN-A9VS                   TCGA-ZN-A9VU 
"DEL PEAK 21(22Q12.2) MUTATED" "DEL PEAK 21(22Q12.2) MUTATED" 
