[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/22507181/MESO-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/MESO-TP/22533663/transformed.cor.cli.txt"

nPatients in clinical file=87, in cluster file=87, common to both=87
[1] 21 87
[1] "DEL PEAK  1(1P36.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            33                             54 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            33                             54 
[1] "DEL PEAK  2(1P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                           37                            50 
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                           37                            50 
[1] "DEL PEAK  3(2Q35) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                         17                          70 
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                         17                          70 
[1] "DEL PEAK  4(3P21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                           48                            39 
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                           48                            39 
[1] "DEL PEAK  5(4Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                         38                          49 
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                         38                          49 
[1] "DEL PEAK  6(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           41                            46 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           41                            46 
[1] "DEL PEAK  7(5Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE 
                           17                            70 
  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE 
                           17                            70 
[1] "DEL PEAK  8(6Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE 
                           41                            46 
  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE 
                           41                            46 
[1] "DEL PEAK  9(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                         36                          51 
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                         36                          51 
[1] "DEL PEAK 10(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                           18                            69 
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                           18                            69 
[1] "DEL PEAK 11(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                           51                            36 
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                           51                            36 
[1] "DEL PEAK 12(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                            28                             59 
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                            28                             59 
[1] "DEL PEAK 13(10Q25.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                            31                             56 
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                            31                             56 
[1] "DEL PEAK 14(11Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE 
                            18                             69 
  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE 
                            18                             69 
[1] "DEL PEAK 15(12P13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE 
                             11                              76 
  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE 
                             11                              76 
[1] "DEL PEAK 16(13Q14.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE 
                             44                              43 
  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE 
                             44                              43 
[1] "DEL PEAK 17(14Q32.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE 
                             39                              48 
  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE 
                             39                              48 
[1] "DEL PEAK 18(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE 
                            28                             59 
  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE 
                            28                             59 
[1] "DEL PEAK 19(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                             6                             81 
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                             6                             81 
[1] "DEL PEAK 20(16Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE 
                            22                             65 
  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE 
                            22                             65 
[1] "DEL PEAK 21(22Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE 
                            68                             19 
  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE 
                            68                             19 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "KARNOFSKY_PERFORMANCE_SCORE"         
[14] "HISTOLOGICAL_TYPE"                   
[15] "RESIDUAL_TUMOR"                      
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 87 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=70,	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=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'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"                       "85"   
freq.contrast "86"    "86"                      "2"    
both >= 3     "FALSE" "FALSE"                   "FALSE"
Variable 17:'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)"
[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 87 columns, 1 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"              "PATHOLOGIC_STAGE"           
 [3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
 [5] "PATHOLOGY_M_STAGE"           "GENDER"                     
 [7] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
 [9] "HISTOLOGICAL_TYPE"           "RESIDUAL_TUMOR"             
YEARS_TO_BIRTH, nv=36, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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 26 32 13 
[1] "table(vv)"
vv
T1 T2 T3 T4 
14 26 32 13 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 T4 
14 26 32 13 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
14 26 32 13 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
44 10 26  3 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
   44    10    29 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 N3 
44 10 26  3 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
   44    10    29 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=5, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = DEL PEAK  1(1P36.31) MUTATION ANALYSIS
D1V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.31) MUTATED    1 31
  DEL PEAK  1(1P36.31) WILD-TYPE 11 42
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            32                             53 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            31                             42 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-UD-AAC4 TCGA-3H-AB3M TCGA-3H-AB3X TCGA-3U-A98F TCGA-LK-A4NY TCGA-LK-A4NZ 
       23.64        29.10        48.99        17.62         5.52         8.02 
TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LI 
        6.08         1.87        12.72        14.73        11.51        18.81 
TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A9CU 
        5.19        10.95        19.99        13.61        23.90        24.07 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A8AF TCGA-TS-A8AI 
        8.38        27.75        41.46         9.30        11.77        10.78 
TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88E TCGA-XT-AASU TCGA-YS-A95B 
        8.32        14.99        13.35        14.27         4.67         1.28 
TCGA-YS-A95C TCGA-ZN-A9VW 
        4.37         2.76 

$`DEL PEAK  1(1P36.31) WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3T TCGA-3H-AB3U 
       26.14        27.06        56.38        11.87        13.61        27.16 
TCGA-3U-A98D TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW TCGA-MQ-A4KX 
        4.67        38.01        28.27        24.36        17.95        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       91.73        23.31        17.33         3.52        24.89        77.56 
TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR 
       68.71         0.66        28.96         2.56         9.76        38.40 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7P1 TCGA-TS-A7P3 
       15.09         7.99        14.76        55.07        18.51        22.65 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ 
       19.43        15.02        32.28        15.42        27.72         6.48 
TCGA-UD-AAC1 TCGA-UT-A88C TCGA-UT-A88G TCGA-UT-A97Y TCGA-YS-AA4M TCGA-ZN-A9VO 
       25.94        28.37         2.50         4.73         2.76         8.58 
TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV 
        7.50        16.41        40.37        32.12        43.04 

  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 
                         48.99                          91.73 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        12.245                         22.650 
[1] "1.3 - 49.0 (12.2)" "0.7 - 91.7 (22.6)"
[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        18
  DEL PEAK  1(1P36.31) WILD-TYPE       5        1        1        9        27
                                vv
clus                             STAGE IV
  DEL PEAK  1(1P36.31) MUTATED          5
  DEL PEAK  1(1P36.31) WILD-TYPE       11
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                           18                             27
  STAGE IV                             5                             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  1(1P36.31) MUTATED    4 10 15  4
  DEL PEAK  1(1P36.31) WILD-TYPE 10 16 17  9
D1V4, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  T1                            4                             10
  T2                           10                             16
  T3                           15                             17
  T4                            4                              9
[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   17  4    10
  DEL PEAK  1(1P36.31) WILD-TYPE 27  6    19
D1V5, multiclass
       clus
vv      DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  N0                              17                             27
  N1                               4                              6
  N2+N3                           10                             19
[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   24  0
  DEL PEAK  1(1P36.31) WILD-TYPE 33  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     24    0
  DEL PEAK  1(1P36.31) WILD-TYPE   33    3
   clus
vv  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  0                           24                             33
  1                            0                              3
[1] 2 2
[1] FALSE
D1V7, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.31) MUTATED    7 26
  DEL PEAK  1(1P36.31) WILD-TYPE  9 45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      7   26
  DEL PEAK  1(1P36.31) WILD-TYPE    9   45
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  FEMALE                            7                              9
  MALE                             26                             45
[1] 2 2
[1] FALSE
D1V8, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.31) MUTATED   24  8
  DEL PEAK  1(1P36.31) WILD-TYPE 38 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     24    8
  DEL PEAK  1(1P36.31) WILD-TYPE   38   16
     clus
vv    DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  NO                            24                             38
  YES                            8                             16
[1] 2 2
[1] FALSE
D1V9, continuous
                                vv
clus                             BIPHASIC MESOTHELIOMA
  DEL PEAK  1(1P36.31) MUTATED                       9
  DEL PEAK  1(1P36.31) WILD-TYPE                    14
                                vv
clus                             DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK  1(1P36.31) MUTATED                                      1
  DEL PEAK  1(1P36.31) WILD-TYPE                                    4
                                vv
clus                             EPITHELIOID MESOTHELIOMA
  DEL PEAK  1(1P36.31) MUTATED                         22
  DEL PEAK  1(1P36.31) WILD-TYPE                       35
                                vv
clus                             SARCOMATOID MESOTHELIOMA
  DEL PEAK  1(1P36.31) MUTATED                          1
  DEL PEAK  1(1P36.31) WILD-TYPE                        1
D1V10, multiclass
                                      clus
vv                                     DEL PEAK  1(1P36.31) MUTATED
  BIPHASIC MESOTHELIOMA                                           9
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                            1
  EPITHELIOID MESOTHELIOMA                                       22
  SARCOMATOID MESOTHELIOMA                                        1
                                      clus
vv                                     DEL PEAK  1(1P36.31) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                            14
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                              4
  EPITHELIOID MESOTHELIOMA                                         35
  SARCOMATOID MESOTHELIOMA                                          1
[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                             R0 R1 R2 RX
  DEL PEAK  1(1P36.31) MUTATED    8  2  7  4
  DEL PEAK  1(1P36.31) WILD-TYPE  9  1  8  7
D1V11, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  R0                            8                              9
  R1                            2                              1
  R2                            7                              8
  RX                            4                              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"

Clustering(2) Variable = DEL PEAK  2(1P21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(1P21.3) MUTATED    0 37
  DEL PEAK  2(1P21.3) WILD-TYPE 12 36
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                           37                            48 
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                           37                            36 
$`DEL PEAK  2(1P21.3) MUTATED`
TCGA-3H-AB3S TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3T TCGA-3U-A98D 
       12.66        27.06        56.38        29.10        13.61         4.67 
TCGA-3U-A98F TCGA-3U-A98J TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O6 
       17.62        24.36         5.52         6.08         1.87        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A6BL 
       11.51        91.73        18.81        23.31        17.33        10.95 
TCGA-MQ-A6BS TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BD TCGA-SH-A9CT TCGA-TS-A7OZ 
       19.99        28.96        13.61        15.09        14.76        27.75 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-TS-A8AF 
       18.51        22.65         9.30        19.43        32.28        11.77 
TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UD-AAC7 
       10.78        15.42        27.72         6.48         8.32        13.35 
TCGA-YS-A95B 
        1.28 

$`DEL PEAK  2(1P21.3) WILD-TYPE`
TCGA-3H-AB3O TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z TCGA-TS-A8AS 
       42.81        62.99        20.71        31.20        21.83        26.14 
TCGA-UD-AAC4 TCGA-3H-AB3L TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98H TCGA-3U-A98I 
       23.64        11.87        27.16        48.99        38.01        28.27 
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LM TCGA-MQ-A4LV 
       17.95         8.02        12.72        80.84         5.19         3.52 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LP TCGA-SC-A6LQ 
       24.89        77.56        68.71         0.66         2.56         9.76 
TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY 
       38.40        23.90         7.99        24.07        55.07         8.38 
TCGA-TS-A7P0 TCGA-TS-A7P8 TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88E 
       41.46        15.02        25.94        14.99        28.37        14.27 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO 
        2.50         4.73         4.67         4.37         2.76         8.58 
TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
        7.50        16.41        40.37        32.12        43.04         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 
                        15.09                         21.27 
[1] "1.3 - 91.7 (15.1)" "0.7 - 80.8 (21.3)"
[1] "hr=" "1.7"
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  2(1P21.3) MUTATED         3        1        0       10        19
  DEL PEAK  2(1P21.3) WILD-TYPE       4        1        1        6        26
                               vv
clus                            STAGE IV
  DEL PEAK  2(1P21.3) MUTATED          4
  DEL PEAK  2(1P21.3) WILD-TYPE       12
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                          19                            26
  STAGE IV                            4                            12
[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 15 15  3
  DEL PEAK  2(1P21.3) WILD-TYPE 10 11 17 10
D2V4, multiclass
    clus
vv   DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE
  T1                           4                            10
  T2                          15                            11
  T3                          15                            17
  T4                           3                            10
[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   20  6    10
  DEL PEAK  2(1P21.3) WILD-TYPE 24  4    19
D2V5, multiclass
       clus
vv      DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE
  N0                             20                            24
  N1                              6                             4
  N2+N3                          10                            19
[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   26  1
  DEL PEAK  2(1P21.3) WILD-TYPE 31  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P21.3) MUTATED     26    1
  DEL PEAK  2(1P21.3) WILD-TYPE   31    2
   clus
vv  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE
  0                          26                            31
  1                           1                             2
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P21.3) MUTATED    8 29
  DEL PEAK  2(1P21.3) WILD-TYPE  8 42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P21.3) MUTATED      8   29
  DEL PEAK  2(1P21.3) WILD-TYPE    8   42
        clus
vv       DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE
  FEMALE                           8                             8
  MALE                            29                            42
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P21.3) MUTATED   24 13
  DEL PEAK  2(1P21.3) WILD-TYPE 38 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P21.3) MUTATED     24   13
  DEL PEAK  2(1P21.3) WILD-TYPE   38   11
     clus
vv    DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE
  NO                           24                            38
  YES                          13                            11
[1] 2 2
[1] FALSE
D2V9, continuous
                               vv
clus                            BIPHASIC MESOTHELIOMA
  DEL PEAK  2(1P21.3) MUTATED                       9
  DEL PEAK  2(1P21.3) WILD-TYPE                    14
                               vv
clus                            DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK  2(1P21.3) MUTATED                                      2
  DEL PEAK  2(1P21.3) WILD-TYPE                                    3
                               vv
clus                            EPITHELIOID MESOTHELIOMA
  DEL PEAK  2(1P21.3) MUTATED                         25
  DEL PEAK  2(1P21.3) WILD-TYPE                       32
                               vv
clus                            SARCOMATOID MESOTHELIOMA
  DEL PEAK  2(1P21.3) MUTATED                          1
  DEL PEAK  2(1P21.3) WILD-TYPE                        1
D2V10, multiclass
                                      clus
vv                                     DEL PEAK  2(1P21.3) MUTATED
  BIPHASIC MESOTHELIOMA                                          9
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                           2
  EPITHELIOID MESOTHELIOMA                                      25
  SARCOMATOID MESOTHELIOMA                                       1
                                      clus
vv                                     DEL PEAK  2(1P21.3) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                           14
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                             3
  EPITHELIOID MESOTHELIOMA                                        32
  SARCOMATOID MESOTHELIOMA                                         1
[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                            R0 R1 R2 RX
  DEL PEAK  2(1P21.3) MUTATED    7  1  5  4
  DEL PEAK  2(1P21.3) WILD-TYPE 10  2 10  7
D2V11, multiclass
    clus
vv   DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE
  R0                           7                            10
  R1                           1                             2
  R2                           5                            10
  RX                           4                             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"

Clustering(3) Variable = DEL PEAK  3(2Q35) MUTATION ANALYSIS
D3V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  3(2Q35) MUTATED    0 17
  DEL PEAK  3(2Q35) WILD-TYPE 12 56
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                         17                          68 
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                         17                          56 
$`DEL PEAK  3(2Q35) MUTATED`
TCGA-3H-AB3S TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3U-A98D TCGA-3U-A98I TCGA-LK-A4NY 
       12.66        11.87        29.10         4.67        28.27         5.52 
TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4LI TCGA-SC-A6LQ TCGA-SH-A7BH 
        6.08         1.87        12.72        18.81         9.76         7.99 
TCGA-SH-A9CU TCGA-TS-A7P1 TCGA-TS-A7P6 TCGA-UD-AABY TCGA-UD-AAC7 
       24.07        18.51         9.30        27.72        13.35 

$`DEL PEAK  3(2Q35) WILD-TYPE`
TCGA-3H-AB3O TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z TCGA-TS-A8AS 
       42.81        62.99        20.71        31.20        21.83        26.14 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X 
       23.64        27.06        56.38        13.61        27.16        48.99 
TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O6 
       17.62        38.01        24.36        17.95         8.02        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
       11.51        80.84        91.73        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS 
        3.52        10.95        24.89        77.56        68.71        19.99 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SH-A7BC 
        0.66        28.96        13.61         2.56        38.40        23.90 
TCGA-SH-A7BD TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 
       15.09        14.76        55.07         8.38        27.75        41.46 
TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
       22.65        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88C 
       15.42         6.48        25.94         8.32        14.99        28.37 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       14.27         2.50         4.73         4.67         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        2.76         8.58         7.50        16.41        40.37        32.12 
TCGA-ZN-A9VV TCGA-ZN-A9VW 
       43.04         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                       18.69 
[1] "1.9 - 29.1 (12.7)" "0.7 - 91.7 (18.7)"
[1] "hr=" "2.1"
D3V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  3(2Q35) MUTATED         1        1        0        3        10
  DEL PEAK  3(2Q35) WILD-TYPE       6        1        1       13        35
                             vv
clus                          STAGE IV
  DEL PEAK  3(2Q35) MUTATED          2
  DEL PEAK  3(2Q35) WILD-TYPE       14
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                        10                          35
  STAGE IV                          2                          14
[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  4  8  2
  DEL PEAK  3(2Q35) WILD-TYPE 12 22 24 11
D3V4, multiclass
    clus
vv   DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  T1                         2                          12
  T2                         4                          22
  T3                         8                          24
  T4                         2                          11
[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     7
  DEL PEAK  3(2Q35) WILD-TYPE 34 10    22
D3V5, multiclass
       clus
vv      DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  N0                           10                          34
  N1                            0                          10
  N2+N3                         7                          22
[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   15  0
  DEL PEAK  3(2Q35) WILD-TYPE 42  3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(2Q35) MUTATED     15    0
  DEL PEAK  3(2Q35) WILD-TYPE   42    3
   clus
vv  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  0                        15                          42
  1                         0                           3
[1] 2 2
[1] FALSE
D3V7, binary
                             cls
clus                           0  1
  DEL PEAK  3(2Q35) MUTATED    7 10
  DEL PEAK  3(2Q35) WILD-TYPE  9 61
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(2Q35) MUTATED      7   10
  DEL PEAK  3(2Q35) WILD-TYPE    9   61
        clus
vv       DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  FEMALE                         7                           9
  MALE                          10                          61
[1] 2 2
[1] FALSE
D3V8, binary
                             cls
clus                           0  1
  DEL PEAK  3(2Q35) MUTATED   14  3
  DEL PEAK  3(2Q35) WILD-TYPE 48 21
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(2Q35) MUTATED     14    3
  DEL PEAK  3(2Q35) WILD-TYPE   48   21
     clus
vv    DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  NO                         14                          48
  YES                         3                          21
[1] 2 2
[1] FALSE
D3V9, continuous
[1] "Remove cluster labels:"    "DEL PEAK  3(2Q35) MUTATED"
clus
  DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE 
                          2                          15 
                 TCGA-3U-A98E                  TCGA-UT-A88D 
"DEL PEAK  3(2Q35) WILD-TYPE" "DEL PEAK  3(2Q35) WILD-TYPE" 
                 TCGA-3U-A98J                  TCGA-SC-A6LM 
"DEL PEAK  3(2Q35) WILD-TYPE" "DEL PEAK  3(2Q35) WILD-TYPE" 
                 TCGA-SC-A6LN                  TCGA-SC-A6LP 
"DEL PEAK  3(2Q35) WILD-TYPE" "DEL PEAK  3(2Q35) WILD-TYPE" 
                 TCGA-SC-A6LR                  TCGA-SH-A9CT 
"DEL PEAK  3(2Q35) WILD-TYPE" "DEL PEAK  3(2Q35) WILD-TYPE" 
                 TCGA-UT-A88C                  TCGA-XT-AASU 
"DEL PEAK  3(2Q35) WILD-TYPE" "DEL PEAK  3(2Q35) WILD-TYPE" 
                 TCGA-ZN-A9VO                  TCGA-ZN-A9VP 
"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" 
                             vv
clus                          BIPHASIC MESOTHELIOMA
  DEL PEAK  3(2Q35) MUTATED                       4
  DEL PEAK  3(2Q35) WILD-TYPE                    19
                             vv
clus                          DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK  3(2Q35) MUTATED                                      1
  DEL PEAK  3(2Q35) WILD-TYPE                                    4
                             vv
clus                          EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  DEL PEAK  3(2Q35) MUTATED                         11                        1
  DEL PEAK  3(2Q35) WILD-TYPE                       46                        1
D3V10, multiclass
                                      clus
vv                                     DEL PEAK  3(2Q35) MUTATED
  BIPHASIC MESOTHELIOMA                                        4
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                         1
  EPITHELIOID MESOTHELIOMA                                    11
  SARCOMATOID MESOTHELIOMA                                     1
                                      clus
vv                                     DEL PEAK  3(2Q35) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                         19
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                           4
  EPITHELIOID MESOTHELIOMA                                      46
  SARCOMATOID MESOTHELIOMA                                       1
[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                          R0 R1 R2 RX
  DEL PEAK  3(2Q35) MUTATED    3  2  3  2
  DEL PEAK  3(2Q35) WILD-TYPE 14  1 12  9
D3V11, multiclass
    clus
vv   DEL PEAK  3(2Q35) MUTATED DEL PEAK  3(2Q35) WILD-TYPE
  R0                         3                          14
  R1                         2                           1
  R2                         3                          12
  RX                         2                           9
[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"

Clustering(4) Variable = DEL PEAK  4(3P21.1) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(3P21.1) MUTATED    7 41
  DEL PEAK  4(3P21.1) WILD-TYPE  5 32
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                           48                            37 
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                           41                            32 
$`DEL PEAK  4(3P21.1) MUTATED`
TCGA-3H-AB3S TCGA-3U-A98E TCGA-UD-AAC4 TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T 
       12.66        62.99        23.64        11.87        29.10        13.61 
TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 
       17.62        38.01        28.27        17.95         8.02         1.87 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LM 
       12.72        14.73        11.51        80.84        91.73         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BS TCGA-NQ-A57I 
       17.33         3.52        10.95        24.89        19.99         0.66 
TCGA-SC-A6LM TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A7BD TCGA-TS-A7OU TCGA-TS-A7P1 
       28.96         9.76        23.90        15.09        55.07        18.51 
TCGA-TS-A7P3 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-UD-AABZ TCGA-UD-AAC5 
       22.65        32.28        11.77        10.78         6.48         8.32 
TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E TCGA-XT-AASU TCGA-ZN-A9VO 
       14.99        13.35        28.37        14.27         4.67         8.58 
TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
        7.50        16.41        40.37        32.12        43.04         2.76 

$`DEL PEAK  4(3P21.1) WILD-TYPE`
TCGA-3H-AB3O TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z TCGA-TS-A8AS TCGA-UT-A88D 
       42.81        20.71        31.20        21.83        26.14        27.06 
TCGA-3H-AB3K TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98J TCGA-LK-A4NY 
       56.38        27.16        48.99         4.67        24.36         5.52 
TCGA-LK-A4O0 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LN 
        6.08        18.81        23.31        77.56        68.71        13.61 
TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OY 
        2.56        38.40         7.99        14.76        24.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A8AY 
       27.75        41.46         9.30        19.43        15.02        15.42 
TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UT-A88G TCGA-UT-A97Y TCGA-YS-A95B TCGA-YS-A95C 
       27.72        25.94         2.50         4.73         1.28         4.37 
TCGA-YS-AA4M 
        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                         77.56 
  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE 
                        15.04                         20.71 
[1] "0.7 - 91.7 (15.0)" "1.3 - 77.6 (20.7)"
[1] "hr=" "1"  
D4V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  4(3P21.1) MUTATED         6        0        1        9        22
  DEL PEAK  4(3P21.1) WILD-TYPE       1        2        0        7        23
                               vv
clus                            STAGE IV
  DEL PEAK  4(3P21.1) MUTATED         10
  DEL PEAK  4(3P21.1) WILD-TYPE        6
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                          22                            23
  STAGE IV                           10                             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  4(3P21.1) MUTATED    7 13 18  9
  DEL PEAK  4(3P21.1) WILD-TYPE  7 13 14  4
D4V4, multiclass
    clus
vv   DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  T1                           7                             7
  T2                          13                            13
  T3                          18                            14
  T4                           9                             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  4(3P21.1) MUTATED   25  4    16
  DEL PEAK  4(3P21.1) WILD-TYPE 19  6    13
D4V5, multiclass
       clus
vv      DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  N0                             25                            19
  N1                              4                             6
  N2+N3                          16                            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"
D4V6, binary
                               cls
clus                             0  1
  DEL PEAK  4(3P21.1) MUTATED   30  2
  DEL PEAK  4(3P21.1) WILD-TYPE 27  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P21.1) MUTATED     30    2
  DEL PEAK  4(3P21.1) WILD-TYPE   27    1
   clus
vv  DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  0                          30                            27
  1                           2                             1
[1] 2 2
[1] FALSE
D4V7, binary
                               cls
clus                             0  1
  DEL PEAK  4(3P21.1) MUTATED    8 40
  DEL PEAK  4(3P21.1) WILD-TYPE  8 31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P21.1) MUTATED      8   40
  DEL PEAK  4(3P21.1) WILD-TYPE    8   31
        clus
vv       DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  FEMALE                           8                             8
  MALE                            40                            31
[1] 2 2
[1] FALSE
D4V8, binary
                               cls
clus                             0  1
  DEL PEAK  4(3P21.1) MUTATED   34 14
  DEL PEAK  4(3P21.1) WILD-TYPE 28 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P21.1) MUTATED     34   14
  DEL PEAK  4(3P21.1) WILD-TYPE   28   10
     clus
vv    DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  NO                           34                            28
  YES                          14                            10
[1] 2 2
[1] FALSE
D4V9, continuous
                               vv
clus                            BIPHASIC MESOTHELIOMA
  DEL PEAK  4(3P21.1) MUTATED                      16
  DEL PEAK  4(3P21.1) WILD-TYPE                     7
                               vv
clus                            DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK  4(3P21.1) MUTATED                                      2
  DEL PEAK  4(3P21.1) WILD-TYPE                                    3
                               vv
clus                            EPITHELIOID MESOTHELIOMA
  DEL PEAK  4(3P21.1) MUTATED                         30
  DEL PEAK  4(3P21.1) WILD-TYPE                       27
                               vv
clus                            SARCOMATOID MESOTHELIOMA
  DEL PEAK  4(3P21.1) MUTATED                          0
  DEL PEAK  4(3P21.1) WILD-TYPE                        2
D4V10, multiclass
                                      clus
vv                                     DEL PEAK  4(3P21.1) MUTATED
  BIPHASIC MESOTHELIOMA                                         16
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                           2
  EPITHELIOID MESOTHELIOMA                                      30
  SARCOMATOID MESOTHELIOMA                                       0
                                      clus
vv                                     DEL PEAK  4(3P21.1) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                            7
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                             3
  EPITHELIOID MESOTHELIOMA                                        27
  SARCOMATOID MESOTHELIOMA                                         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                            R0 R1 R2 RX
  DEL PEAK  4(3P21.1) MUTATED    9  1  9  5
  DEL PEAK  4(3P21.1) WILD-TYPE  8  2  6  6
D4V11, multiclass
    clus
vv   DEL PEAK  4(3P21.1) MUTATED DEL PEAK  4(3P21.1) WILD-TYPE
  R0                           9                             8
  R1                           1                             2
  R2                           9                             6
  RX                           5                             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"

Clustering(5) Variable = DEL PEAK  5(4Q26) MUTATION ANALYSIS
D5V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  5(4Q26) MUTATED    2 36
  DEL PEAK  5(4Q26) WILD-TYPE 10 37
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                         38                          47 
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                         36                          37 
$`DEL PEAK  5(4Q26) MUTATED`
TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98I 
       11.87        29.10        13.61         4.67        17.62        28.27 
TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LI 
        6.08         1.87        12.72        14.73        11.51        18.81 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BR TCGA-MQ-A6BS 
        5.19        17.33         3.52        10.95        68.71        19.99 
TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OY 
       13.61        23.90         7.99        14.76        24.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A8AF 
       27.75        41.46        18.51         9.30        19.43        11.77 
TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88G 
       10.78        15.42         6.48         8.32        13.35         2.50 
TCGA-UT-A97Y TCGA-ZN-A9VS 
        4.73        40.37 

$`DEL PEAK  5(4Q26) WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3U TCGA-3H-AB3X 
       26.14        23.64        27.06        56.38        27.16        48.99 
TCGA-3U-A98H TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-MQ-A4KX 
       38.01        24.36        17.95         5.52         8.02        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LJ TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-NQ-A57I TCGA-SC-A6LM 
       91.73        23.31        24.89        77.56         0.66        28.96 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BD TCGA-TS-A7OU TCGA-TS-A7P3 
        2.56         9.76        38.40        15.09        55.07        22.65 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UT-A88C 
       15.02        32.28        27.72        25.94        14.99        28.37 
TCGA-UT-A88E TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO 
       14.27         4.67         1.28         4.37         2.76         8.58 
TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
        7.50        16.41        32.12        43.04         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 
                      68.71                       91.73 
  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE 
                      13.48                       23.64 
[1] "1.9 - 68.7 (13.5)" "0.7 - 91.7 (23.6)"
[1] "hr=" "2.2"
D5V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  5(4Q26) MUTATED         4        1        0        6        23
  DEL PEAK  5(4Q26) WILD-TYPE       3        1        1       10        22
                             vv
clus                          STAGE IV
  DEL PEAK  5(4Q26) MUTATED          4
  DEL PEAK  5(4Q26) WILD-TYPE       12
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                        23                          22
  STAGE IV                          4                          12
[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  9 19  3
  DEL PEAK  5(4Q26) WILD-TYPE  8 17 13 10
D5V4, multiclass
    clus
vv   DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  T1                         6                           8
  T2                         9                          17
  T3                        19                          13
  T4                         3                          10
[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   21  6    11
  DEL PEAK  5(4Q26) WILD-TYPE 23  4    18
D5V5, multiclass
       clus
vv      DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  N0                           21                          23
  N1                            6                           4
  N2+N3                        11                          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"
D5V6, binary
                             cls
clus                           0  1
  DEL PEAK  5(4Q26) MUTATED   26  0
  DEL PEAK  5(4Q26) WILD-TYPE 31  3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(4Q26) MUTATED     26    0
  DEL PEAK  5(4Q26) WILD-TYPE   31    3
   clus
vv  DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  0                        26                          31
  1                         0                           3
[1] 2 2
[1] FALSE
D5V7, binary
                             cls
clus                           0  1
  DEL PEAK  5(4Q26) MUTATED    9 29
  DEL PEAK  5(4Q26) WILD-TYPE  7 42
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(4Q26) MUTATED      9   29
  DEL PEAK  5(4Q26) WILD-TYPE    7   42
        clus
vv       DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  FEMALE                         9                           7
  MALE                          29                          42
[1] 2 2
[1] FALSE
D5V8, binary
                             cls
clus                           0  1
  DEL PEAK  5(4Q26) MUTATED   29  9
  DEL PEAK  5(4Q26) WILD-TYPE 33 15
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(4Q26) MUTATED     29    9
  DEL PEAK  5(4Q26) WILD-TYPE   33   15
     clus
vv    DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  NO                         29                          33
  YES                         9                          15
[1] 2 2
[1] FALSE
D5V9, continuous
                             vv
clus                          BIPHASIC MESOTHELIOMA
  DEL PEAK  5(4Q26) MUTATED                      12
  DEL PEAK  5(4Q26) WILD-TYPE                    11
                             vv
clus                          DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK  5(4Q26) MUTATED                                      0
  DEL PEAK  5(4Q26) WILD-TYPE                                    5
                             vv
clus                          EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  DEL PEAK  5(4Q26) MUTATED                         25                        1
  DEL PEAK  5(4Q26) WILD-TYPE                       32                        1
D5V10, multiclass
                                      clus
vv                                     DEL PEAK  5(4Q26) MUTATED
  BIPHASIC MESOTHELIOMA                                       12
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                         0
  EPITHELIOID MESOTHELIOMA                                    25
  SARCOMATOID MESOTHELIOMA                                     1
                                      clus
vv                                     DEL PEAK  5(4Q26) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                         11
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                           5
  EPITHELIOID MESOTHELIOMA                                      32
  SARCOMATOID MESOTHELIOMA                                       1
[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                          R0 R1 R2 RX
  DEL PEAK  5(4Q26) MUTATED    5  2  4  7
  DEL PEAK  5(4Q26) WILD-TYPE 12  1 11  4
D5V11, multiclass
    clus
vv   DEL PEAK  5(4Q26) MUTATED DEL PEAK  5(4Q26) WILD-TYPE
  R0                         5                          12
  R1                         2                           1
  R2                         4                          11
  RX                         7                           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"

Clustering(6) Variable = DEL PEAK  6(4Q34.3) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(4Q34.3) MUTATED    3 38
  DEL PEAK  6(4Q34.3) WILD-TYPE  9 35
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           41                            44 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           38                            35 
$`DEL PEAK  6(4Q34.3) MUTATED`
TCGA-UD-AAC4 TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T TCGA-3H-AB3X TCGA-3U-A98D 
       23.64        11.87        29.10        13.61        48.99         4.67 
TCGA-3U-A98F TCGA-3U-A98I TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-LK-A4O6 
       17.62        28.27         5.52         6.08        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A6BL TCGA-MQ-A6BR 
       11.51        18.81         5.19        17.33        10.95        68.71 
TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU 
       19.99        13.61        23.90         7.99        14.76        24.07 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A8AF 
        8.38        27.75        41.46         9.30        19.43        11.77 
TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
       10.78        15.42         6.48         8.32        14.99        13.35 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-ZN-A9VS TCGA-ZN-A9VW 
       14.27         2.50         4.73        40.37         2.76 

$`DEL PEAK  6(4Q34.3) WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3U TCGA-3U-A98H TCGA-3U-A98J 
       26.14        27.06        56.38        27.16        38.01        24.36 
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LJ 
       17.95         8.02         1.87        80.84        91.73        23.31 
TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP 
        3.52        24.89        77.56         0.66        28.96         2.56 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BD TCGA-TS-A7OU TCGA-TS-A7P1 TCGA-TS-A7P3 
        9.76        38.40        15.09        55.07        18.51        22.65 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UT-A88C TCGA-XT-AASU 
       15.02        32.28        27.72        25.94        28.37         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ 
        1.28         4.37         2.76         8.58         7.50        16.41 
TCGA-ZN-A9VU TCGA-ZN-A9VV 
       32.12        43.04 

  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 
                        68.71                         91.73 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                       13.610                        23.835 
[1] "2.5 - 68.7 (13.6)" "0.7 - 91.7 (23.8)"
[1] "hr=" "2"  
D6V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  6(4Q34.3) MUTATED         4        1        0        7        24
  DEL PEAK  6(4Q34.3) WILD-TYPE       3        1        1        9        21
                               vv
clus                            STAGE IV
  DEL PEAK  6(4Q34.3) MUTATED          5
  DEL PEAK  6(4Q34.3) WILD-TYPE       11
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                          24                            21
  STAGE IV                            5                            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  6(4Q34.3) MUTATED    6 11 19  4
  DEL PEAK  6(4Q34.3) WILD-TYPE  8 15 13  9
D6V4, multiclass
    clus
vv   DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  T1                           6                             8
  T2                          11                            15
  T3                          19                            13
  T4                           4                             9
[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   23  6    12
  DEL PEAK  6(4Q34.3) WILD-TYPE 21  4    17
D6V5, multiclass
       clus
vv      DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  N0                             23                            21
  N1                              6                             4
  N2+N3                          12                            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"
D6V6, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q34.3) MUTATED   29  0
  DEL PEAK  6(4Q34.3) WILD-TYPE 28  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED     29    0
  DEL PEAK  6(4Q34.3) WILD-TYPE   28    3
   clus
vv  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  0                          29                            28
  1                           0                             3
[1] 2 2
[1] FALSE
D6V7, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q34.3) MUTATED    9 32
  DEL PEAK  6(4Q34.3) WILD-TYPE  7 39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED      9   32
  DEL PEAK  6(4Q34.3) WILD-TYPE    7   39
        clus
vv       DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  FEMALE                           9                             7
  MALE                            32                            39
[1] 2 2
[1] FALSE
D6V8, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q34.3) MUTATED   30 11
  DEL PEAK  6(4Q34.3) WILD-TYPE 32 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED     30   11
  DEL PEAK  6(4Q34.3) WILD-TYPE   32   13
     clus
vv    DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  NO                           30                            32
  YES                          11                            13
[1] 2 2
[1] FALSE
D6V9, continuous
                               vv
clus                            BIPHASIC MESOTHELIOMA
  DEL PEAK  6(4Q34.3) MUTATED                      14
  DEL PEAK  6(4Q34.3) WILD-TYPE                     9
                               vv
clus                            DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK  6(4Q34.3) MUTATED                                      1
  DEL PEAK  6(4Q34.3) WILD-TYPE                                    4
                               vv
clus                            EPITHELIOID MESOTHELIOMA
  DEL PEAK  6(4Q34.3) MUTATED                         25
  DEL PEAK  6(4Q34.3) WILD-TYPE                       32
                               vv
clus                            SARCOMATOID MESOTHELIOMA
  DEL PEAK  6(4Q34.3) MUTATED                          1
  DEL PEAK  6(4Q34.3) WILD-TYPE                        1
D6V10, multiclass
                                      clus
vv                                     DEL PEAK  6(4Q34.3) MUTATED
  BIPHASIC MESOTHELIOMA                                         14
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                           1
  EPITHELIOID MESOTHELIOMA                                      25
  SARCOMATOID MESOTHELIOMA                                       1
                                      clus
vv                                     DEL PEAK  6(4Q34.3) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                            9
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                             4
  EPITHELIOID MESOTHELIOMA                                        32
  SARCOMATOID MESOTHELIOMA                                         1
[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                            R0 R1 R2 RX
  DEL PEAK  6(4Q34.3) MUTATED    5  2  5  8
  DEL PEAK  6(4Q34.3) WILD-TYPE 12  1 10  3
D6V11, multiclass
    clus
vv   DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  R0                           5                            12
  R1                           2                             1
  R2                           5                            10
  RX                           8                             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"

Clustering(7) Variable = DEL PEAK  7(5Q23.2) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  7(5Q23.2) MUTATED    0 17
  DEL PEAK  7(5Q23.2) WILD-TYPE 12 56
  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE 
                           17                            68 
  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE 
                           17                            56 
$`DEL PEAK  7(5Q23.2) MUTATED`
TCGA-3H-AB3L TCGA-3U-A98D TCGA-3U-A98F TCGA-LK-A4O7 TCGA-MQ-A4LV TCGA-MQ-A6BS 
       11.87         4.67        17.62        11.51         3.52        19.99 
TCGA-SC-A6LN TCGA-SC-A6LQ TCGA-SH-A7BD TCGA-SH-A9CU TCGA-TS-A7P0 TCGA-TS-A7P1 
       13.61         9.76        15.09        24.07        41.46        18.51 
TCGA-TS-A8AF TCGA-TS-A8AI TCGA-UD-AABZ TCGA-UD-AAC7 TCGA-XT-AASU 
       11.77        10.78         6.48        13.35         4.67 

$`DEL PEAK  7(5Q23.2) WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3T 
       26.14        23.64        27.06        56.38        29.10        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW 
       27.16        48.99        38.01        28.27        24.36        17.95 
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-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
       80.84        91.73        18.81        23.31         5.19        17.33 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM 
       10.95        24.89        77.56        68.71         0.66        28.96 
TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU 
        2.56        38.40        23.90         7.99        14.76        55.07 
TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 
        8.38        27.75        22.65         9.30        19.43        15.02 
TCGA-TS-A7PB TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 
       32.28        15.42        27.72        25.94         8.32        14.99 
TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-YS-A95B TCGA-YS-A95C 
       28.37        14.27         2.50         4.73         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        2.76         8.58         7.50        16.41        40.37        32.12 
TCGA-ZN-A9VV TCGA-ZN-A9VW 
       43.04         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                         20.07 
[1] "3.5 - 41.5 (11.9)" "0.7 - 91.7 (20.1)"
[1] "hr=" "2.4"
D7V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  7(5Q23.2) MUTATED         1        0        0        3        10
  DEL PEAK  7(5Q23.2) WILD-TYPE       6        2        1       13        35
                               vv
clus                            STAGE IV
  DEL PEAK  7(5Q23.2) MUTATED          3
  DEL PEAK  7(5Q23.2) WILD-TYPE       13
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                          10                            35
  STAGE IV                            3                            13
[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  7  6  2
  DEL PEAK  7(5Q23.2) WILD-TYPE 13 19 26 11
D7V4, multiclass
    clus
vv   DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE
  T1                           1                            13
  T2                           7                            19
  T3                           6                            26
  T4                           2                            11
[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    8  2     6
  DEL PEAK  7(5Q23.2) WILD-TYPE 36  8    23
D7V5, multiclass
       clus
vv      DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE
  N0                              8                            36
  N1                              2                             8
  N2+N3                           6                            23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                               cls
clus                             0  1
  DEL PEAK  7(5Q23.2) MUTATED   10  1
  DEL PEAK  7(5Q23.2) WILD-TYPE 47  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5Q23.2) MUTATED     10    1
  DEL PEAK  7(5Q23.2) WILD-TYPE   47    2
   clus
vv  DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE
  0                          10                            47
  1                           1                             2
[1] 2 2
[1] FALSE
D7V7, binary
                               cls
clus                             0  1
  DEL PEAK  7(5Q23.2) MUTATED    1 16
  DEL PEAK  7(5Q23.2) WILD-TYPE 15 55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5Q23.2) MUTATED      1   16
  DEL PEAK  7(5Q23.2) WILD-TYPE   15   55
        clus
vv       DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE
  FEMALE                           1                            15
  MALE                            16                            55
[1] 2 2
[1] FALSE
D7V8, binary
                               cls
clus                             0  1
  DEL PEAK  7(5Q23.2) MUTATED   10  7
  DEL PEAK  7(5Q23.2) WILD-TYPE 52 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5Q23.2) MUTATED     10    7
  DEL PEAK  7(5Q23.2) WILD-TYPE   52   17
     clus
vv    DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE
  NO                           10                            52
  YES                           7                            17
[1] 2 2
[1] FALSE
D7V9, continuous
                               vv
clus                            BIPHASIC MESOTHELIOMA
  DEL PEAK  7(5Q23.2) MUTATED                       5
  DEL PEAK  7(5Q23.2) WILD-TYPE                    18
                               vv
clus                            DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK  7(5Q23.2) MUTATED                                      0
  DEL PEAK  7(5Q23.2) WILD-TYPE                                    5
                               vv
clus                            EPITHELIOID MESOTHELIOMA
  DEL PEAK  7(5Q23.2) MUTATED                         12
  DEL PEAK  7(5Q23.2) WILD-TYPE                       45
                               vv
clus                            SARCOMATOID MESOTHELIOMA
  DEL PEAK  7(5Q23.2) MUTATED                          0
  DEL PEAK  7(5Q23.2) WILD-TYPE                        2
D7V10, multiclass
                                      clus
vv                                     DEL PEAK  7(5Q23.2) MUTATED
  BIPHASIC MESOTHELIOMA                                          5
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                           0
  EPITHELIOID MESOTHELIOMA                                      12
  SARCOMATOID MESOTHELIOMA                                       0
                                      clus
vv                                     DEL PEAK  7(5Q23.2) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                           18
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                             5
  EPITHELIOID MESOTHELIOMA                                        45
  SARCOMATOID MESOTHELIOMA                                         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                            R0 R1 R2 RX
  DEL PEAK  7(5Q23.2) MUTATED    6  0  2  2
  DEL PEAK  7(5Q23.2) WILD-TYPE 11  3 13  9
D7V11, multiclass
    clus
vv   DEL PEAK  7(5Q23.2) MUTATED DEL PEAK  7(5Q23.2) WILD-TYPE
  R0                           6                            11
  R1                           0                             3
  R2                           2                            13
  RX                           2                             9
[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"

Clustering(8) Variable = DEL PEAK  8(6Q22.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(6Q22.1) MUTATED    6 34
  DEL PEAK  8(6Q22.1) WILD-TYPE  6 39
  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE 
                           40                            45 
  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE 
                           34                            39 
$`DEL PEAK  8(6Q22.1) MUTATED`
TCGA-3U-A98E TCGA-TS-A8AS TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3U-A98D 
       62.99        26.14        56.38        11.87        29.10         4.67 
TCGA-3U-A98I TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O7 TCGA-MQ-A4KX 
       28.27         8.02         6.08         1.87        11.51        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN 
       91.73        18.81         5.19         3.52        10.95        24.89 
TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CU 
       77.56        19.99         0.66        23.90        15.09        24.07 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-TS-A8AI 
       27.75        41.46         9.30        19.43        32.28        10.78 
TCGA-TS-A8AY TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88G TCGA-XT-AASU 
       15.42         8.32        14.99        13.35         2.50         4.67 
TCGA-ZN-A9VO TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        8.58        16.41        40.37        32.12 

$`DEL PEAK  8(6Q22.1) WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z TCGA-UD-AAC4 
       42.81        12.66        20.71        31.20        21.83        23.64 
TCGA-UT-A88D TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98F TCGA-3U-A98H 
       27.06        13.61        27.16        48.99        17.62        38.01 
TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4LJ 
       24.36        17.95         5.52        12.72        14.73        23.31 
TCGA-MQ-A4LP TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       17.33        68.71        28.96        13.61         2.56         9.76 
TCGA-SC-A6LR TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7P1 
       38.40         7.99        14.76        55.07         8.38        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P8 TCGA-TS-A8AF TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 
       22.65        15.02        11.77        27.72         6.48        25.94 
TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A97Y TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M 
       28.37        14.27         4.73         1.28         4.37         2.76 
TCGA-ZN-A9VP TCGA-ZN-A9VV TCGA-ZN-A9VW 
        7.50        43.04         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                         68.71 
  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE 
                       15.915                        17.620 
[1] "0.7 - 91.7 (15.9)" "1.3 - 68.7 (17.6)"
[1] "hr=" "1.1"
D8V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  8(6Q22.1) MUTATED         3        2        1       11        18
  DEL PEAK  8(6Q22.1) WILD-TYPE       4        0        0        5        27
                               vv
clus                            STAGE IV
  DEL PEAK  8(6Q22.1) MUTATED          6
  DEL PEAK  8(6Q22.1) WILD-TYPE       10
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                          18                            27
  STAGE IV                            6                            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  8(6Q22.1) MUTATED    6 14 15  5
  DEL PEAK  8(6Q22.1) WILD-TYPE  8 12 17  8
D8V4, multiclass
    clus
vv   DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE
  T1                           6                             8
  T2                          14                            12
  T3                          15                            17
  T4                           5                             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  8(6Q22.1) MUTATED   22  5    11
  DEL PEAK  8(6Q22.1) WILD-TYPE 22  5    18
D8V5, multiclass
       clus
vv      DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE
  N0                             22                            22
  N1                              5                             5
  N2+N3                          11                            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"
D8V6, binary
                               cls
clus                             0  1
  DEL PEAK  8(6Q22.1) MUTATED   23  2
  DEL PEAK  8(6Q22.1) WILD-TYPE 34  1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(6Q22.1) MUTATED     23    2
  DEL PEAK  8(6Q22.1) WILD-TYPE   34    1
   clus
vv  DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE
  0                          23                            34
  1                           2                             1
[1] 2 2
[1] FALSE
D8V7, binary
                               cls
clus                             0  1
  DEL PEAK  8(6Q22.1) MUTATED    6 35
  DEL PEAK  8(6Q22.1) WILD-TYPE 10 36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(6Q22.1) MUTATED      6   35
  DEL PEAK  8(6Q22.1) WILD-TYPE   10   36
        clus
vv       DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE
  FEMALE                           6                            10
  MALE                            35                            36
[1] 2 2
[1] FALSE
D8V8, binary
                               cls
clus                             0  1
  DEL PEAK  8(6Q22.1) MUTATED   31  9
  DEL PEAK  8(6Q22.1) WILD-TYPE 31 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(6Q22.1) MUTATED     31    9
  DEL PEAK  8(6Q22.1) WILD-TYPE   31   15
     clus
vv    DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE
  NO                           31                            31
  YES                           9                            15
[1] 2 2
[1] FALSE
D8V9, continuous
                               vv
clus                            BIPHASIC MESOTHELIOMA
  DEL PEAK  8(6Q22.1) MUTATED                      11
  DEL PEAK  8(6Q22.1) WILD-TYPE                    12
                               vv
clus                            DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK  8(6Q22.1) MUTATED                                      1
  DEL PEAK  8(6Q22.1) WILD-TYPE                                    4
                               vv
clus                            EPITHELIOID MESOTHELIOMA
  DEL PEAK  8(6Q22.1) MUTATED                         28
  DEL PEAK  8(6Q22.1) WILD-TYPE                       29
                               vv
clus                            SARCOMATOID MESOTHELIOMA
  DEL PEAK  8(6Q22.1) MUTATED                          1
  DEL PEAK  8(6Q22.1) WILD-TYPE                        1
D8V10, multiclass
                                      clus
vv                                     DEL PEAK  8(6Q22.1) MUTATED
  BIPHASIC MESOTHELIOMA                                         11
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                           1
  EPITHELIOID MESOTHELIOMA                                      28
  SARCOMATOID MESOTHELIOMA                                       1
                                      clus
vv                                     DEL PEAK  8(6Q22.1) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                           12
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                             4
  EPITHELIOID MESOTHELIOMA                                        29
  SARCOMATOID MESOTHELIOMA                                         1
[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                            R0 R1 R2 RX
  DEL PEAK  8(6Q22.1) MUTATED    9  2  7  3
  DEL PEAK  8(6Q22.1) WILD-TYPE  8  1  8  8
D8V11, multiclass
    clus
vv   DEL PEAK  8(6Q22.1) MUTATED DEL PEAK  8(6Q22.1) WILD-TYPE
  R0                           9                             8
  R1                           2                             1
  R2                           7                             8
  RX                           3                             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"

Clustering(9) Variable = DEL PEAK  9(6Q26) MUTATION ANALYSIS
D9V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  9(6Q26) MUTATED    4 31
  DEL PEAK  9(6Q26) WILD-TYPE  8 42
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                         35                          50 
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                         31                          42 
$`DEL PEAK  9(6Q26) MUTATED`
TCGA-3U-A98E TCGA-TS-A8AS TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3U-A98F 
       62.99        26.14        56.38        11.87        29.10        17.62 
TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-MQ-A4KX 
       28.27        24.36         5.52         6.08         1.87        80.84 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BQ TCGA-MQ-A6BS 
       91.73        18.81         5.19        10.95        77.56        19.99 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A9CU TCGA-TS-A7OU 
        0.66        28.96        13.61        23.90        24.07        55.07 
TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-TS-A8AY TCGA-UD-AAC5 
       41.46         9.30        19.43        32.28        15.42         8.32 
TCGA-UD-AAC7 TCGA-UT-A88E TCGA-UT-A88G TCGA-ZN-A9VQ TCGA-ZN-A9VS 
       13.35        14.27         2.50        16.41        40.37 

$`DEL PEAK  9(6Q26) WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z TCGA-UD-AAC4 
       42.81        12.66        20.71        31.20        21.83        23.64 
TCGA-UT-A88D TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98H 
       27.06        13.61        27.16        48.99         4.67        38.01 
TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LJ 
       17.95         8.02        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        68.71         2.56         9.76 
TCGA-SC-A6LR TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OY TCGA-TS-A7OZ 
       38.40        15.09         7.99        14.76         8.38        27.75 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P8 TCGA-TS-A8AF TCGA-TS-A8AI TCGA-UD-AABY 
       18.51        22.65        15.02        11.77        10.78        27.72 
TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A97Y TCGA-XT-AASU 
        6.48        25.94        14.99        28.37         4.73         4.67 
TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VU 
        1.28         4.37         2.76         8.58         7.50        32.12 
TCGA-ZN-A9VV TCGA-ZN-A9VW 
       43.04         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                       68.71 
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                     19.430                      15.005 
[1] "0.7 - 91.7 (19.4)" "1.3 - 68.7 (15.0)"
[1] "hr=" "1.3"
D9V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK  9(6Q26) MUTATED         4        2        1        8        16
  DEL PEAK  9(6Q26) WILD-TYPE       3        0        0        8        29
                             vv
clus                          STAGE IV
  DEL PEAK  9(6Q26) MUTATED          5
  DEL PEAK  9(6Q26) WILD-TYPE       11
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                        16                          29
  STAGE IV                          5                          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  9(6Q26) MUTATED    7  9 14  5
  DEL PEAK  9(6Q26) WILD-TYPE  7 17 18  8
D9V4, multiclass
    clus
vv   DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  T1                         7                           7
  T2                         9                          17
  T3                        14                          18
  T4                         5                           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  9(6Q26) MUTATED   21  1    11
  DEL PEAK  9(6Q26) WILD-TYPE 23  9    18
D9V5, multiclass
       clus
vv      DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  N0                           21                          23
  N1                            1                           9
  N2+N3                        11                          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"
D9V6, binary
                             cls
clus                           0  1
  DEL PEAK  9(6Q26) MUTATED   24  0
  DEL PEAK  9(6Q26) WILD-TYPE 33  3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(6Q26) MUTATED     24    0
  DEL PEAK  9(6Q26) WILD-TYPE   33    3
   clus
vv  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  0                        24                          33
  1                         0                           3
[1] 2 2
[1] FALSE
D9V7, binary
                             cls
clus                           0  1
  DEL PEAK  9(6Q26) MUTATED    7 29
  DEL PEAK  9(6Q26) WILD-TYPE  9 42
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(6Q26) MUTATED      7   29
  DEL PEAK  9(6Q26) WILD-TYPE    9   42
        clus
vv       DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  FEMALE                         7                           9
  MALE                          29                          42
[1] 2 2
[1] FALSE
D9V8, binary
                             cls
clus                           0  1
  DEL PEAK  9(6Q26) MUTATED   27  8
  DEL PEAK  9(6Q26) WILD-TYPE 35 16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(6Q26) MUTATED     27    8
  DEL PEAK  9(6Q26) WILD-TYPE   35   16
     clus
vv    DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  NO                         27                          35
  YES                         8                          16
[1] 2 2
[1] FALSE
D9V9, continuous
                             vv
clus                          BIPHASIC MESOTHELIOMA
  DEL PEAK  9(6Q26) MUTATED                      10
  DEL PEAK  9(6Q26) WILD-TYPE                    13
                             vv
clus                          DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK  9(6Q26) MUTATED                                      1
  DEL PEAK  9(6Q26) WILD-TYPE                                    4
                             vv
clus                          EPITHELIOID MESOTHELIOMA SARCOMATOID MESOTHELIOMA
  DEL PEAK  9(6Q26) MUTATED                         24                        1
  DEL PEAK  9(6Q26) WILD-TYPE                       33                        1
D9V10, multiclass
                                      clus
vv                                     DEL PEAK  9(6Q26) MUTATED
  BIPHASIC MESOTHELIOMA                                       10
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                         1
  EPITHELIOID MESOTHELIOMA                                    24
  SARCOMATOID MESOTHELIOMA                                     1
                                      clus
vv                                     DEL PEAK  9(6Q26) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                         13
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                           4
  EPITHELIOID MESOTHELIOMA                                      33
  SARCOMATOID MESOTHELIOMA                                       1
[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                          R0 R1 R2 RX
  DEL PEAK  9(6Q26) MUTATED    7  2  5  4
  DEL PEAK  9(6Q26) WILD-TYPE 10  1 10  7
D9V11, multiclass
    clus
vv   DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  R0                         7                          10
  R1                         2                           1
  R2                         5                          10
  RX                         4                           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"

Clustering(10) Variable = DEL PEAK 10(8P23.2) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 10(8P23.2) MUTATED    2 16
  DEL PEAK 10(8P23.2) WILD-TYPE 10 57
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                           18                            67 
  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE 
                           16                            57 
$`DEL PEAK 10(8P23.2) MUTATED`
TCGA-SC-AA5Z TCGA-UD-AAC4 TCGA-3H-AB3K TCGA-3U-A98D TCGA-3U-A98J TCGA-LK-A4O0 
       21.83        23.64        56.38         4.67        24.36         6.08 
TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-SC-A6LN TCGA-SC-A6LQ 
       91.73        18.81        77.56        19.99        13.61         9.76 
TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-UD-AAC5 TCGA-ZN-A9VW 
       24.07        55.07        27.75        18.51         8.32         2.76 

$`DEL PEAK 10(8P23.2) WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-TS-A8AS 
       42.81        12.66        62.99        20.71        31.20        26.14 
TCGA-UT-A88D TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X 
       27.06        11.87        29.10        13.61        27.16        48.99 
TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ 
       17.62        38.01        28.27        17.95         5.52         8.02 
TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LJ 
        1.87        12.72        14.73        11.51        80.84        23.31 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BR 
        5.19        17.33         3.52        10.95        24.89        68.71 
TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD 
        0.66        28.96         2.56        38.40        23.90        15.09 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OY TCGA-TS-A7P0 TCGA-TS-A7P3 TCGA-TS-A7P6 
        7.99        14.76         8.38        41.46        22.65         9.30 
TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI TCGA-TS-A8AY 
       19.43        15.02        32.28        11.77        10.78        15.42 
TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
       27.72         6.48        25.94        14.99        13.35        28.37 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       14.27         2.50         4.73         4.67         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        2.76         8.58         7.50        16.41        40.37        32.12 
TCGA-ZN-A9VV 
       43.04 

  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 
                        20.91                         15.09 
[1] "2.8 - 91.7 (20.9)" "0.7 - 80.8 (15.1)"
[1] "hr=" "1.3"
D10V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 10(8P23.2) MUTATED         2        1        0        5         6
  DEL PEAK 10(8P23.2) WILD-TYPE       5        1        1       11        39
                               vv
clus                            STAGE IV
  DEL PEAK 10(8P23.2) MUTATED          4
  DEL PEAK 10(8P23.2) WILD-TYPE       12
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                           6                            39
  STAGE IV                            4                            12
[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  8  3  4
  DEL PEAK 10(8P23.2) WILD-TYPE 11 18 29  9
D10V4, multiclass
    clus
vv   DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  T1                           3                            11
  T2                           8                            18
  T3                           3                            29
  T4                           4                             9
[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     7
  DEL PEAK 10(8P23.2) WILD-TYPE 34  9    22
D10V5, multiclass
       clus
vv      DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  N0                             10                            34
  N1                              1                             9
  N2+N3                           7                            22
[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   12  0
  DEL PEAK 10(8P23.2) WILD-TYPE 45  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(8P23.2) MUTATED     12    0
  DEL PEAK 10(8P23.2) WILD-TYPE   45    3
   clus
vv  DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  0                          12                            45
  1                           0                             3
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                             0  1
  DEL PEAK 10(8P23.2) MUTATED    2 16
  DEL PEAK 10(8P23.2) WILD-TYPE 14 55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(8P23.2) MUTATED      2   16
  DEL PEAK 10(8P23.2) WILD-TYPE   14   55
        clus
vv       DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  FEMALE                           2                            14
  MALE                            16                            55
[1] 2 2
[1] FALSE
D10V8, binary
                               cls
clus                             0  1
  DEL PEAK 10(8P23.2) MUTATED   12  6
  DEL PEAK 10(8P23.2) WILD-TYPE 50 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(8P23.2) MUTATED     12    6
  DEL PEAK 10(8P23.2) WILD-TYPE   50   18
     clus
vv    DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  NO                           12                            50
  YES                           6                            18
[1] 2 2
[1] FALSE
D10V9, continuous
                               vv
clus                            BIPHASIC MESOTHELIOMA
  DEL PEAK 10(8P23.2) MUTATED                       3
  DEL PEAK 10(8P23.2) WILD-TYPE                    20
                               vv
clus                            DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK 10(8P23.2) MUTATED                                      2
  DEL PEAK 10(8P23.2) WILD-TYPE                                    3
                               vv
clus                            EPITHELIOID MESOTHELIOMA
  DEL PEAK 10(8P23.2) MUTATED                         12
  DEL PEAK 10(8P23.2) WILD-TYPE                       45
                               vv
clus                            SARCOMATOID MESOTHELIOMA
  DEL PEAK 10(8P23.2) MUTATED                          1
  DEL PEAK 10(8P23.2) WILD-TYPE                        1
D10V10, multiclass
                                      clus
vv                                     DEL PEAK 10(8P23.2) MUTATED
  BIPHASIC MESOTHELIOMA                                          3
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                           2
  EPITHELIOID MESOTHELIOMA                                      12
  SARCOMATOID MESOTHELIOMA                                       1
                                      clus
vv                                     DEL PEAK 10(8P23.2) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                           20
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                             3
  EPITHELIOID MESOTHELIOMA                                        45
  SARCOMATOID MESOTHELIOMA                                         1
[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                            R0 R1 R2 RX
  DEL PEAK 10(8P23.2) MUTATED    5  2  2  2
  DEL PEAK 10(8P23.2) WILD-TYPE 12  1 13  9
D10V11, multiclass
    clus
vv   DEL PEAK 10(8P23.2) MUTATED DEL PEAK 10(8P23.2) WILD-TYPE
  R0                           5                            12
  R1                           2                             1
  R2                           2                            13
  RX                           2                             9
[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"

Clustering(11) Variable = DEL PEAK 11(9P21.3) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 11(9P21.3) MUTATED    3 47
  DEL PEAK 11(9P21.3) WILD-TYPE  9 26
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                           50                            35 
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                           47                            26 
$`DEL PEAK 11(9P21.3) MUTATED`
TCGA-3H-AB3S TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3T 
       12.66        23.64        27.06        11.87        29.10        13.61 
TCGA-3U-A98D TCGA-3U-A98F TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-LK-A4O2 
        4.67        17.62        17.95         5.52         6.08         1.87 
TCGA-LK-A4O5 TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
       12.72        11.51        18.81        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
        3.52        10.95        19.99         0.66        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A9CU TCGA-TS-A7OY TCGA-TS-A7OZ 
        2.56         9.76        23.90        24.07         8.38        27.75 
TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A8AF TCGA-TS-A8AI 
       41.46        18.51         9.30        19.43        11.77        10.78 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 
       15.42        27.72         6.48         8.32        14.99        13.35 
TCGA-UT-A88E TCGA-UT-A88G TCGA-XT-AASU TCGA-YS-A95B TCGA-ZN-A9VP TCGA-ZN-A9VQ 
       14.27         2.50         4.67         1.28         7.50        16.41 
TCGA-ZN-A9VS TCGA-ZN-A9VW 
       40.37         2.76 

$`DEL PEAK 11(9P21.3) WILD-TYPE`
TCGA-3H-AB3O TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z TCGA-TS-A8AS 
       42.81        62.99        20.71        31.20        21.83        26.14 
TCGA-3H-AB3K TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J 
       56.38        27.16        48.99        38.01        28.27        24.36 
TCGA-LK-A4NZ TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A6BN TCGA-MQ-A6BQ 
        8.02        14.73        80.84        91.73        24.89        77.56 
TCGA-MQ-A6BR TCGA-SC-A6LR TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7OU 
       68.71        38.40        15.09         7.99        14.76        55.07 
TCGA-TS-A7P3 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-UD-AAC1 TCGA-UT-A88C TCGA-UT-A97Y 
       22.65        15.02        32.28        25.94        28.37         4.73 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VU TCGA-ZN-A9VV 
        4.37         2.76         8.58        32.12        43.04 

  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                         0.66                          2.76 
  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 
                       13.035                        27.160 
[1] "0.7 - 41.5 (13.0)" "2.8 - 91.7 (27.2)"
[1] "hr=" "3.6"
D11V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 11(9P21.3) MUTATED         5        1        1       10        27
  DEL PEAK 11(9P21.3) WILD-TYPE       2        1        0        6        18
                               vv
clus                            STAGE IV
  DEL PEAK 11(9P21.3) MUTATED          7
  DEL PEAK 11(9P21.3) WILD-TYPE        9
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                          27                            18
  STAGE IV                            7                             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 11(9P21.3) MUTATED    7 15 22  6
  DEL PEAK 11(9P21.3) WILD-TYPE  7 11 10  7
D11V4, multiclass
    clus
vv   DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  T1                           7                             7
  T2                          15                            11
  T3                          22                            10
  T4                           6                             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 11(9P21.3) MUTATED   27  5    15
  DEL PEAK 11(9P21.3) WILD-TYPE 17  5    14
D11V5, multiclass
       clus
vv      DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  N0                             27                            17
  N1                              5                             5
  N2+N3                          15                            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"
D11V6, binary
                               cls
clus                             0  1
  DEL PEAK 11(9P21.3) MUTATED   35  0
  DEL PEAK 11(9P21.3) WILD-TYPE 22  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(9P21.3) MUTATED     35    0
  DEL PEAK 11(9P21.3) WILD-TYPE   22    3
   clus
vv  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  0                          35                            22
  1                           0                             3
[1] 2 2
[1] FALSE
D11V7, binary
                               cls
clus                             0  1
  DEL PEAK 11(9P21.3) MUTATED    9 42
  DEL PEAK 11(9P21.3) WILD-TYPE  7 29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(9P21.3) MUTATED      9   42
  DEL PEAK 11(9P21.3) WILD-TYPE    7   29
        clus
vv       DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  FEMALE                           9                             7
  MALE                            42                            29
[1] 2 2
[1] FALSE
D11V8, binary
                               cls
clus                             0  1
  DEL PEAK 11(9P21.3) MUTATED   36 14
  DEL PEAK 11(9P21.3) WILD-TYPE 26 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(9P21.3) MUTATED     36   14
  DEL PEAK 11(9P21.3) WILD-TYPE   26   10
     clus
vv    DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  NO                           36                            26
  YES                          14                            10
[1] 2 2
[1] FALSE
D11V9, continuous
                               vv
clus                            BIPHASIC MESOTHELIOMA
  DEL PEAK 11(9P21.3) MUTATED                      16
  DEL PEAK 11(9P21.3) WILD-TYPE                     7
                               vv
clus                            DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK 11(9P21.3) MUTATED                                      3
  DEL PEAK 11(9P21.3) WILD-TYPE                                    2
                               vv
clus                            EPITHELIOID MESOTHELIOMA
  DEL PEAK 11(9P21.3) MUTATED                         31
  DEL PEAK 11(9P21.3) WILD-TYPE                       26
                               vv
clus                            SARCOMATOID MESOTHELIOMA
  DEL PEAK 11(9P21.3) MUTATED                          1
  DEL PEAK 11(9P21.3) WILD-TYPE                        1
D11V10, multiclass
                                      clus
vv                                     DEL PEAK 11(9P21.3) MUTATED
  BIPHASIC MESOTHELIOMA                                         16
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                           3
  EPITHELIOID MESOTHELIOMA                                      31
  SARCOMATOID MESOTHELIOMA                                       1
                                      clus
vv                                     DEL PEAK 11(9P21.3) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                            7
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                             2
  EPITHELIOID MESOTHELIOMA                                        26
  SARCOMATOID MESOTHELIOMA                                         1
[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                            R0 R1 R2 RX
  DEL PEAK 11(9P21.3) MUTATED   10  2  8  8
  DEL PEAK 11(9P21.3) WILD-TYPE  7  1  7  3
D11V11, multiclass
    clus
vv   DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  R0                          10                             7
  R1                           2                             1
  R2                           8                             7
  RX                           8                             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"

Clustering(12) Variable = DEL PEAK 12(10P15.3) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 12(10P15.3) MUTATED    1 26
  DEL PEAK 12(10P15.3) WILD-TYPE 11 47
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                            27                             58 
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                            26                             47 
$`DEL PEAK 12(10P15.3) MUTATED`
TCGA-3H-AB3L TCGA-3U-A98D TCGA-3U-A98I TCGA-LK-A4NY TCGA-LK-A4O2 TCGA-LK-A4O7 
       11.87         4.67        28.27         5.52         1.87        11.51 
TCGA-MQ-A4LM TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SH-A7BH 
        5.19        17.33         3.52        19.99         0.66         7.99 
TCGA-SH-A9CU TCGA-TS-A7P1 TCGA-TS-A7P6 TCGA-TS-A7P8 TCGA-TS-A8AF TCGA-TS-A8AI 
       24.07        18.51         9.30        15.02        11.77        10.78 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AAC5 TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
       15.42        27.72         8.32        14.27         2.50         4.73 
TCGA-XT-AASU TCGA-ZN-A9VQ TCGA-ZN-A9VW 
        4.67        16.41         2.76 

$`DEL PEAK 12(10P15.3) WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3T 
       26.14        23.64        27.06        56.38        29.10        13.61 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98J TCGA-LK-A4NW 
       27.16        48.99        17.62        38.01        24.36        17.95 
TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        8.02         6.08        12.72        14.73        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       18.81        23.31        10.95        24.89        77.56        68.71 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC 
       28.96        13.61         2.56         9.76        38.40        23.90 
TCGA-SH-A7BD TCGA-SH-A9CT TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 
       15.09        14.76        55.07         8.38        27.75        41.46 
TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC6 
       22.65        19.43        32.28         6.48        25.94        14.99 
TCGA-UD-AAC7 TCGA-UT-A88C TCGA-YS-A95B TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO 
       13.35        28.37         1.28         4.37         2.76         8.58 
TCGA-ZN-A9VP TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV 
        7.50        40.37        32.12        43.04 

  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 
                         28.27                          91.73 
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                        10.780                         23.475 
[1] "0.7 - 28.3 (10.8)" "1.3 - 91.7 (23.5)"
[1] "hr=" "3.5"
D12V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 12(10P15.3) MUTATED         5        0        1        2        16
  DEL PEAK 12(10P15.3) WILD-TYPE       2        2        0       14        29
                                vv
clus                             STAGE IV
  DEL PEAK 12(10P15.3) MUTATED          4
  DEL PEAK 12(10P15.3) WILD-TYPE       12
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                           16                             29
  STAGE IV                             4                             12
[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  4 12  4
  DEL PEAK 12(10P15.3) WILD-TYPE  8 22 20  9
D12V4, multiclass
    clus
vv   DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE
  T1                            6                              8
  T2                            4                             22
  T3                           12                             20
  T4                            4                              9
[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     6
  DEL PEAK 12(10P15.3) WILD-TYPE 29  6    23
D12V5, multiclass
       clus
vv      DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE
  N0                              15                             29
  N1                               4                              6
  N2+N3                            6                             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                                cls
clus                              0  1
  DEL PEAK 12(10P15.3) MUTATED   17  0
  DEL PEAK 12(10P15.3) WILD-TYPE 40  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(10P15.3) MUTATED     17    0
  DEL PEAK 12(10P15.3) WILD-TYPE   40    3
   clus
vv  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE
  0                           17                             40
  1                            0                              3
[1] 2 2
[1] FALSE
D12V7, binary
                                cls
clus                              0  1
  DEL PEAK 12(10P15.3) MUTATED    5 23
  DEL PEAK 12(10P15.3) WILD-TYPE 11 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(10P15.3) MUTATED      5   23
  DEL PEAK 12(10P15.3) WILD-TYPE   11   48
        clus
vv       DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE
  FEMALE                            5                             11
  MALE                             23                             48
[1] 2 2
[1] FALSE
D12V8, binary
                                cls
clus                              0  1
  DEL PEAK 12(10P15.3) MUTATED   25  2
  DEL PEAK 12(10P15.3) WILD-TYPE 37 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(10P15.3) MUTATED     25    2
  DEL PEAK 12(10P15.3) WILD-TYPE   37   22
     clus
vv    DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE
  NO                            25                             37
  YES                            2                             22
[1] 2 2
[1] FALSE
D12V9, continuous
                                vv
clus                             BIPHASIC MESOTHELIOMA
  DEL PEAK 12(10P15.3) MUTATED                      12
  DEL PEAK 12(10P15.3) WILD-TYPE                    11
                                vv
clus                             DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK 12(10P15.3) MUTATED                                      1
  DEL PEAK 12(10P15.3) WILD-TYPE                                    4
                                vv
clus                             EPITHELIOID MESOTHELIOMA
  DEL PEAK 12(10P15.3) MUTATED                         15
  DEL PEAK 12(10P15.3) WILD-TYPE                       42
                                vv
clus                             SARCOMATOID MESOTHELIOMA
  DEL PEAK 12(10P15.3) MUTATED                          0
  DEL PEAK 12(10P15.3) WILD-TYPE                        2
D12V10, multiclass
                                      clus
vv                                     DEL PEAK 12(10P15.3) MUTATED
  BIPHASIC MESOTHELIOMA                                          12
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                            1
  EPITHELIOID MESOTHELIOMA                                       15
  SARCOMATOID MESOTHELIOMA                                        0
                                      clus
vv                                     DEL PEAK 12(10P15.3) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                            11
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                              4
  EPITHELIOID MESOTHELIOMA                                         42
  SARCOMATOID MESOTHELIOMA                                          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                             R0 R1 R2 RX
  DEL PEAK 12(10P15.3) MUTATED    6  0  3  6
  DEL PEAK 12(10P15.3) WILD-TYPE 11  3 12  5
D12V11, multiclass
    clus
vv   DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE
  R0                            6                             11
  R1                            0                              3
  R2                            3                             12
  RX                            6                              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"

Clustering(13) Variable = DEL PEAK 13(10Q25.2) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 13(10Q25.2) MUTATED    2 28
  DEL PEAK 13(10Q25.2) WILD-TYPE 10 45
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                            30                             55 
  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE 
                            28                             45 
$`DEL PEAK 13(10Q25.2) MUTATED`
TCGA-UT-A88D TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3U-A98D TCGA-LK-A4NY TCGA-LK-A4O7 
       27.06        11.87        29.10         4.67         5.52        11.51 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM 
       17.33         3.52        24.89        19.99         0.66        28.96 
TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7P6 
       15.09         7.99        14.76        24.07        55.07         9.30 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-UD-AABY TCGA-UD-AAC5 TCGA-UD-AAC7 
       15.02        32.28        10.78        27.72         8.32        13.35 
TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VW 
        2.50         4.73         4.67         8.58         7.50         2.76 

$`DEL PEAK 13(10Q25.2) WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-3H-AB3K TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X 
       26.14        23.64        56.38        13.61        27.16        48.99 
TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NZ 
       17.62        38.01        28.27        24.36        17.95         8.02 
TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC 
        6.08         1.87        12.72        14.73        80.84        91.73 
TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BQ TCGA-MQ-A6BR 
       18.81        23.31         5.19        10.95        77.56        68.71 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BC TCGA-TS-A7OY 
       13.61         2.56         9.76        38.40        23.90         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A8AF 
       27.75        41.46        18.51        22.65        19.43        11.77 
TCGA-TS-A8AY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UT-A88C TCGA-UT-A88E 
       15.42         6.48        25.94        14.99        28.37        14.27 
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        40.37        32.12 
TCGA-ZN-A9VV 
       43.04 

  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 
                         11.69                          20.71 
[1] "0.7 - 55.1 (11.7)" "1.3 - 91.7 (20.7)"
[1] "hr=" "2"  
D13V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 13(10Q25.2) MUTATED         2        0        1        5        16
  DEL PEAK 13(10Q25.2) WILD-TYPE       5        2        0       11        29
                                vv
clus                             STAGE IV
  DEL PEAK 13(10Q25.2) MUTATED          7
  DEL PEAK 13(10Q25.2) WILD-TYPE        9
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                           16                             29
  STAGE IV                             7                              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 13(10Q25.2) MUTATED    3  8 12  6
  DEL PEAK 13(10Q25.2) WILD-TYPE 11 18 20  7
D13V4, multiclass
    clus
vv   DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  T1                            3                             11
  T2                            8                             18
  T3                           12                             20
  T4                            6                              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 13(10Q25.2) MUTATED   15  4     8
  DEL PEAK 13(10Q25.2) WILD-TYPE 29  6    21
D13V5, multiclass
       clus
vv      DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  N0                              15                             29
  N1                               4                              6
  N2+N3                            8                             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"
D13V6, binary
                                cls
clus                              0  1
  DEL PEAK 13(10Q25.2) MUTATED   18  2
  DEL PEAK 13(10Q25.2) WILD-TYPE 39  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q25.2) MUTATED     18    2
  DEL PEAK 13(10Q25.2) WILD-TYPE   39    1
   clus
vv  DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  0                           18                             39
  1                            2                              1
[1] 2 2
[1] FALSE
D13V7, binary
                                cls
clus                              0  1
  DEL PEAK 13(10Q25.2) MUTATED    6 25
  DEL PEAK 13(10Q25.2) WILD-TYPE 10 46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q25.2) MUTATED      6   25
  DEL PEAK 13(10Q25.2) WILD-TYPE   10   46
        clus
vv       DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  FEMALE                            6                             10
  MALE                             25                             46
[1] 2 2
[1] FALSE
D13V8, binary
                                cls
clus                              0  1
  DEL PEAK 13(10Q25.2) MUTATED   23  7
  DEL PEAK 13(10Q25.2) WILD-TYPE 39 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q25.2) MUTATED     23    7
  DEL PEAK 13(10Q25.2) WILD-TYPE   39   17
     clus
vv    DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  NO                            23                             39
  YES                            7                             17
[1] 2 2
[1] FALSE
D13V9, continuous
                                vv
clus                             BIPHASIC MESOTHELIOMA
  DEL PEAK 13(10Q25.2) MUTATED                      10
  DEL PEAK 13(10Q25.2) WILD-TYPE                    13
                                vv
clus                             DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK 13(10Q25.2) MUTATED                                      1
  DEL PEAK 13(10Q25.2) WILD-TYPE                                    4
                                vv
clus                             EPITHELIOID MESOTHELIOMA
  DEL PEAK 13(10Q25.2) MUTATED                         20
  DEL PEAK 13(10Q25.2) WILD-TYPE                       37
                                vv
clus                             SARCOMATOID MESOTHELIOMA
  DEL PEAK 13(10Q25.2) MUTATED                          0
  DEL PEAK 13(10Q25.2) WILD-TYPE                        2
D13V10, multiclass
                                      clus
vv                                     DEL PEAK 13(10Q25.2) MUTATED
  BIPHASIC MESOTHELIOMA                                          10
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                            1
  EPITHELIOID MESOTHELIOMA                                       20
  SARCOMATOID MESOTHELIOMA                                        0
                                      clus
vv                                     DEL PEAK 13(10Q25.2) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                            13
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                              4
  EPITHELIOID MESOTHELIOMA                                         37
  SARCOMATOID MESOTHELIOMA                                          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                             R0 R1 R2 RX
  DEL PEAK 13(10Q25.2) MUTATED    8  0  5  5
  DEL PEAK 13(10Q25.2) WILD-TYPE  9  3 10  6
D13V11, multiclass
    clus
vv   DEL PEAK 13(10Q25.2) MUTATED DEL PEAK 13(10Q25.2) WILD-TYPE
  R0                            8                              9
  R1                            0                              3
  R2                            5                             10
  RX                            5                              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"

Clustering(14) Variable = DEL PEAK 14(11Q23.2) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 14(11Q23.2) MUTATED    1 16
  DEL PEAK 14(11Q23.2) WILD-TYPE 11 57
  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE 
                            17                             68 
  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE 
                            16                             57 
$`DEL PEAK 14(11Q23.2) MUTATED`
TCGA-3H-AB3S TCGA-3H-AB3M TCGA-3H-AB3T TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98J 
       12.66        29.10        13.61        48.99         4.67        24.36 
TCGA-LK-A4NW TCGA-LK-A4O0 TCGA-LK-A4O7 TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-NQ-A57I 
       17.95         6.08        11.51         5.19         3.52         0.66 
TCGA-SC-A6LQ TCGA-SH-A9CT TCGA-TS-A7OZ TCGA-UD-AABY TCGA-UD-AABZ 
        9.76        14.76        27.75        27.72         6.48 

$`DEL PEAK 14(11Q23.2) WILD-TYPE`
TCGA-3H-AB3O TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z TCGA-TS-A8AS 
       42.81        62.99        20.71        31.20        21.83        26.14 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3U TCGA-3U-A98F 
       23.64        27.06        56.38        11.87        27.16        17.62 
TCGA-3U-A98H TCGA-3U-A98I TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 TCGA-LK-A4O5 
       38.01        28.27         5.52         8.02         1.87        12.72 
TCGA-LK-A4O6 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LP 
       14.73        80.84        91.73        18.81        23.31        17.33 
TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS TCGA-SC-A6LM 
       10.95        24.89        77.56        68.71        19.99        28.96 
TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH 
       13.61         2.56        38.40        23.90        15.09         7.99 
TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       24.07        55.07         8.38        41.46        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
        9.30        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AY TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
       15.42        25.94         8.32        14.99        13.35        28.37 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       14.27         2.50         4.73         4.67         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        2.76         8.58         7.50        16.41        40.37        32.12 
TCGA-ZN-A9VV TCGA-ZN-A9VW 
       43.04         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 
                         48.99                          91.73 
  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE 
                         12.66                          18.66 
[1] "0.7 - 49.0 (12.7)" "1.3 - 91.7 (18.7)"
[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        10
  DEL PEAK 14(11Q23.2) WILD-TYPE       6        1        0       12        35
                                vv
clus                             STAGE IV
  DEL PEAK 14(11Q23.2) MUTATED          1
  DEL PEAK 14(11Q23.2) WILD-TYPE       15
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                           10                             35
  STAGE IV                             1                             15
[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  5  9  1
  DEL PEAK 14(11Q23.2) WILD-TYPE 11 21 23 12
D14V4, multiclass
    clus
vv   DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE
  T1                            3                             11
  T2                            5                             21
  T3                            9                             23
  T4                            1                             12
[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     5
  DEL PEAK 14(11Q23.2) WILD-TYPE 35  8    24
D14V5, multiclass
       clus
vv      DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE
  N0                               9                             35
  N1                               2                              8
  N2+N3                            5                             24
[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   16  0
  DEL PEAK 14(11Q23.2) WILD-TYPE 41  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q23.2) MUTATED     16    0
  DEL PEAK 14(11Q23.2) WILD-TYPE   41    3
   clus
vv  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE
  0                           16                             41
  1                            0                              3
[1] 2 2
[1] FALSE
D14V7, binary
                                cls
clus                              0  1
  DEL PEAK 14(11Q23.2) MUTATED    2 16
  DEL PEAK 14(11Q23.2) WILD-TYPE 14 55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q23.2) MUTATED      2   16
  DEL PEAK 14(11Q23.2) WILD-TYPE   14   55
        clus
vv       DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE
  FEMALE                            2                             14
  MALE                             16                             55
[1] 2 2
[1] FALSE
D14V8, binary
                                cls
clus                              0  1
  DEL PEAK 14(11Q23.2) MUTATED   11  6
  DEL PEAK 14(11Q23.2) WILD-TYPE 51 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q23.2) MUTATED     11    6
  DEL PEAK 14(11Q23.2) WILD-TYPE   51   18
     clus
vv    DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE
  NO                            11                             51
  YES                            6                             18
[1] 2 2
[1] FALSE
D14V9, continuous
[1] "Remove cluster labels:"       "DEL PEAK 14(11Q23.2) MUTATED"
clus
  DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE 
                             2                             15 
                    TCGA-3U-A98E                     TCGA-UT-A88D 
"DEL PEAK 14(11Q23.2) WILD-TYPE" "DEL PEAK 14(11Q23.2) WILD-TYPE" 
                    TCGA-SC-A6LM                     TCGA-SC-A6LN 
"DEL PEAK 14(11Q23.2) WILD-TYPE" "DEL PEAK 14(11Q23.2) WILD-TYPE" 
                    TCGA-SC-A6LP                     TCGA-SC-A6LR 
"DEL PEAK 14(11Q23.2) WILD-TYPE" "DEL PEAK 14(11Q23.2) WILD-TYPE" 
                    TCGA-SH-A7BH                     TCGA-SH-A9CU 
"DEL PEAK 14(11Q23.2) WILD-TYPE" "DEL PEAK 14(11Q23.2) WILD-TYPE" 
                    TCGA-UT-A88C                     TCGA-XT-AASU 
"DEL PEAK 14(11Q23.2) WILD-TYPE" "DEL PEAK 14(11Q23.2) WILD-TYPE" 
                    TCGA-ZN-A9VO                     TCGA-ZN-A9VP 
"DEL PEAK 14(11Q23.2) WILD-TYPE" "DEL PEAK 14(11Q23.2) WILD-TYPE" 
                    TCGA-ZN-A9VQ                     TCGA-ZN-A9VS 
"DEL PEAK 14(11Q23.2) WILD-TYPE" "DEL PEAK 14(11Q23.2) WILD-TYPE" 
                    TCGA-ZN-A9VU 
"DEL PEAK 14(11Q23.2) WILD-TYPE" 
                                vv
clus                             BIPHASIC MESOTHELIOMA
  DEL PEAK 14(11Q23.2) MUTATED                       5
  DEL PEAK 14(11Q23.2) WILD-TYPE                    18
                                vv
clus                             DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK 14(11Q23.2) MUTATED                                      2
  DEL PEAK 14(11Q23.2) WILD-TYPE                                    3
                                vv
clus                             EPITHELIOID MESOTHELIOMA
  DEL PEAK 14(11Q23.2) MUTATED                         10
  DEL PEAK 14(11Q23.2) WILD-TYPE                       47
                                vv
clus                             SARCOMATOID MESOTHELIOMA
  DEL PEAK 14(11Q23.2) MUTATED                          1
  DEL PEAK 14(11Q23.2) WILD-TYPE                        1
D14V10, multiclass
                                      clus
vv                                     DEL PEAK 14(11Q23.2) MUTATED
  BIPHASIC MESOTHELIOMA                                           5
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                            2
  EPITHELIOID MESOTHELIOMA                                       10
  SARCOMATOID MESOTHELIOMA                                        1
                                      clus
vv                                     DEL PEAK 14(11Q23.2) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                            18
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                              3
  EPITHELIOID MESOTHELIOMA                                         47
  SARCOMATOID MESOTHELIOMA                                          1
[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                             R0 R1 R2 RX
  DEL PEAK 14(11Q23.2) MUTATED    5  0  1  3
  DEL PEAK 14(11Q23.2) WILD-TYPE 12  3 14  8
D14V11, multiclass
    clus
vv   DEL PEAK 14(11Q23.2) MUTATED DEL PEAK 14(11Q23.2) WILD-TYPE
  R0                            5                             12
  R1                            0                              3
  R2                            1                             14
  RX                            3                              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"

Clustering(15) Variable = DEL PEAK 15(12P13.31) MUTATION ANALYSIS
D15V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 15(12P13.31) MUTATED    0 11
  DEL PEAK 15(12P13.31) WILD-TYPE 12 62
  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE 
                             11                              74 
  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE 
                             11                              62 
$`DEL PEAK 15(12P13.31) MUTATED`
TCGA-3H-AB3T TCGA-3U-A98D TCGA-3U-A98F TCGA-LK-A4O7 TCGA-NQ-A57I TCGA-SH-A7BC 
       13.61         4.67        17.62        11.51         0.66        23.90 
TCGA-SH-A7BH TCGA-SH-A9CT TCGA-TS-A7P0 TCGA-UD-AAC7 TCGA-ZN-A9VW 
        7.99        14.76        41.46        13.35         2.76 

$`DEL PEAK 15(12P13.31) WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW 
       27.16        48.99        38.01        28.27        24.36        17.95 
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-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LP 
       80.84        91.73        18.81        23.31         5.19        17.33 
TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-MQ-A6BS 
        3.52        10.95        24.89        77.56        68.71        19.99 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BD 
       28.96        13.61         2.56         9.76        38.40        15.09 
TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P1 TCGA-TS-A7P3 
       24.07        55.07         8.38        27.75        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
        9.30        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 
       15.42        27.72         6.48        25.94         8.32        14.99 
TCGA-UT-A88C TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B 
       28.37        14.27         2.50         4.73         4.67         1.28 
TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS 
        4.37         2.76         8.58         7.50        16.41        40.37 
TCGA-ZN-A9VU TCGA-ZN-A9VV 
       32.12        43.04 

  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                           18.66 
[1] "0.7 - 41.5 (13.3)" "1.3 - 91.7 (18.7)"
[1] "hr=" "2.2"
D15V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 15(12P13.31) MUTATED         1        0        1        2         6
  DEL PEAK 15(12P13.31) WILD-TYPE       6        2        0       14        39
                                 vv
clus                              STAGE IV
  DEL PEAK 15(12P13.31) MUTATED          1
  DEL PEAK 15(12P13.31) WILD-TYPE       15
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                             6                              39
  STAGE IV                              1                              15
[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  3  5  1
  DEL PEAK 15(12P13.31) WILD-TYPE 12 23 27 12
D15V4, multiclass
    clus
vv   DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE
  T1                             2                              12
  T2                             3                              23
  T3                             5                              27
  T4                             1                              12
[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    7  1     2
  DEL PEAK 15(12P13.31) WILD-TYPE 37  9    27
D15V5, multiclass
       clus
vv      DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE
  N0                                7                              37
  N1                                1                               9
  N2+N3                             2                              27
[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    8  0
  DEL PEAK 15(12P13.31) WILD-TYPE 49  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(12P13.31) MUTATED      8    0
  DEL PEAK 15(12P13.31) WILD-TYPE   49    3
   clus
vv  DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE
  0                             8                              49
  1                             0                               3
[1] 2 2
[1] FALSE
D15V7, binary
                                 cls
clus                               0  1
  DEL PEAK 15(12P13.31) MUTATED    1 10
  DEL PEAK 15(12P13.31) WILD-TYPE 15 61
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(12P13.31) MUTATED      1   10
  DEL PEAK 15(12P13.31) WILD-TYPE   15   61
        clus
vv       DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE
  FEMALE                             1                              15
  MALE                              10                              61
[1] 2 2
[1] FALSE
D15V8, binary
                                 cls
clus                               0  1
  DEL PEAK 15(12P13.31) MUTATED    6  5
  DEL PEAK 15(12P13.31) WILD-TYPE 56 19
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(12P13.31) MUTATED      6    5
  DEL PEAK 15(12P13.31) WILD-TYPE   56   19
     clus
vv    DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE
  NO                              6                              56
  YES                             5                              19
[1] 2 2
[1] FALSE
D15V9, 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 
                              2                              15 
                     TCGA-3U-A98E                      TCGA-UT-A88D 
"DEL PEAK 15(12P13.31) WILD-TYPE" "DEL PEAK 15(12P13.31) WILD-TYPE" 
                     TCGA-3U-A98J                      TCGA-SC-A6LM 
"DEL PEAK 15(12P13.31) WILD-TYPE" "DEL PEAK 15(12P13.31) WILD-TYPE" 
                     TCGA-SC-A6LN                      TCGA-SC-A6LP 
"DEL PEAK 15(12P13.31) WILD-TYPE" "DEL PEAK 15(12P13.31) WILD-TYPE" 
                     TCGA-SC-A6LR                      TCGA-SH-A9CU 
"DEL PEAK 15(12P13.31) WILD-TYPE" "DEL PEAK 15(12P13.31) WILD-TYPE" 
                     TCGA-UT-A88C                      TCGA-XT-AASU 
"DEL PEAK 15(12P13.31) WILD-TYPE" "DEL PEAK 15(12P13.31) WILD-TYPE" 
                     TCGA-ZN-A9VO                      TCGA-ZN-A9VP 
"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" 
                                 vv
clus                              BIPHASIC MESOTHELIOMA
  DEL PEAK 15(12P13.31) MUTATED                       6
  DEL PEAK 15(12P13.31) WILD-TYPE                    17
                                 vv
clus                              DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK 15(12P13.31) MUTATED                                      0
  DEL PEAK 15(12P13.31) WILD-TYPE                                    5
                                 vv
clus                              EPITHELIOID MESOTHELIOMA
  DEL PEAK 15(12P13.31) MUTATED                          5
  DEL PEAK 15(12P13.31) WILD-TYPE                       52
                                 vv
clus                              SARCOMATOID MESOTHELIOMA
  DEL PEAK 15(12P13.31) MUTATED                          0
  DEL PEAK 15(12P13.31) WILD-TYPE                        2
D15V10, multiclass
                                      clus
vv                                     DEL PEAK 15(12P13.31) MUTATED
  BIPHASIC MESOTHELIOMA                                            6
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                             0
  EPITHELIOID MESOTHELIOMA                                         5
  SARCOMATOID MESOTHELIOMA                                         0
                                      clus
vv                                     DEL PEAK 15(12P13.31) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                             17
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                               5
  EPITHELIOID MESOTHELIOMA                                          52
  SARCOMATOID MESOTHELIOMA                                           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                              R0 R1 R2 RX
  DEL PEAK 15(12P13.31) MUTATED    1  0  4  0
  DEL PEAK 15(12P13.31) WILD-TYPE 16  3 11 11
D15V11, multiclass
    clus
vv   DEL PEAK 15(12P13.31) MUTATED DEL PEAK 15(12P13.31) WILD-TYPE
  R0                             1                              16
  R1                             0                               3
  R2                             4                              11
  RX                             0                              11
[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"

Clustering(16) Variable = DEL PEAK 16(13Q14.11) MUTATION ANALYSIS
D16V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 16(13Q14.11) MUTATED    4 40
  DEL PEAK 16(13Q14.11) WILD-TYPE  8 33
  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE 
                             44                              41 
  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE 
                             40                              33 
$`DEL PEAK 16(13Q14.11) MUTATED`
TCGA-3H-AB3S TCGA-TS-A8AS TCGA-3H-AB3L TCGA-3H-AB3T TCGA-3U-A98I TCGA-LK-A4NW 
       12.66        26.14        11.87        13.61        28.27        17.95 
TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
        6.08         1.87        12.72        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LM TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BS TCGA-SC-A6LN 
       23.31         5.19         3.52        10.95        19.99        13.61 
TCGA-SC-A6LP TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU 
        2.56        23.90        15.09         7.99        14.76        24.07 
TCGA-TS-A7OY TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A8AF 
        8.38        41.46        18.51         9.30        19.43        11.77 
TCGA-TS-A8AI TCGA-TS-A8AY TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88C 
       10.78        15.42         6.48         8.32        13.35        28.37 
TCGA-UT-A88E TCGA-UT-A88G TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VQ TCGA-ZN-A9VS 
       14.27         2.50         2.76         8.58        16.41        40.37 
TCGA-ZN-A9VU TCGA-ZN-A9VW 
       32.12         2.76 

$`DEL PEAK 16(13Q14.11) WILD-TYPE`
TCGA-3H-AB3O TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z TCGA-UD-AAC4 
       42.81        62.99        20.71        31.20        21.83        23.64 
TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3M TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D 
       27.06        56.38        29.10        27.16        48.99         4.67 
TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98J TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O6 
       17.62        38.01        24.36         5.52         8.02        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4LP TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I 
       11.51        17.33        24.89        77.56        68.71         0.66 
TCGA-SC-A6LM TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-TS-A7OU TCGA-TS-A7OZ TCGA-TS-A7P3 
       28.96         9.76        38.40        55.07        27.75        22.65 
TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC6 TCGA-UT-A97Y 
       15.02        32.28        27.72        25.94        14.99         4.73 
TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C TCGA-ZN-A9VP TCGA-ZN-A9VV 
        4.67         1.28         4.37         7.50        43.04 

  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                           77.56 
  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE 
                          13.61                           24.36 
[1] "1.9 - 91.7 (13.6)" "0.7 - 77.6 (24.4)"
[1] "hr=" "1.7"
D16V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 16(13Q14.11) MUTATED         6        2        0       10        17
  DEL PEAK 16(13Q14.11) WILD-TYPE       1        0        1        6        28
                                 vv
clus                              STAGE IV
  DEL PEAK 16(13Q14.11) MUTATED          9
  DEL PEAK 16(13Q14.11) WILD-TYPE        7
D16V3, multiclass
           clus
vv          DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE
  STAGE I                               6                               1
  STAGE IA                              2                               0
  STAGE IB                              0                               1
  STAGE II                             10                               6
  STAGE III                            17                              28
  STAGE IV                              9                               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 16(13Q14.11) MUTATED    9 14 14  6
  DEL PEAK 16(13Q14.11) WILD-TYPE  5 12 18  7
D16V4, multiclass
    clus
vv   DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE
  T1                             9                               5
  T2                            14                              12
  T3                            14                              18
  T4                             6                               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 16(13Q14.11) MUTATED   29  3    12
  DEL PEAK 16(13Q14.11) WILD-TYPE 15  7    17
D16V5, multiclass
       clus
vv      DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE
  N0                               29                              15
  N1                                3                               7
  N2+N3                            12                              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"
D16V6, binary
                                 cls
clus                               0  1
  DEL PEAK 16(13Q14.11) MUTATED   27  3
  DEL PEAK 16(13Q14.11) WILD-TYPE 30  0
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(13Q14.11) MUTATED     27    3
  DEL PEAK 16(13Q14.11) WILD-TYPE   30    0
   clus
vv  DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE
  0                            27                              30
  1                             3                               0
[1] 2 2
[1] FALSE
D16V7, binary
                                 cls
clus                               0  1
  DEL PEAK 16(13Q14.11) MUTATED    5 39
  DEL PEAK 16(13Q14.11) WILD-TYPE 11 32
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(13Q14.11) MUTATED      5   39
  DEL PEAK 16(13Q14.11) WILD-TYPE   11   32
        clus
vv       DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE
  FEMALE                             5                              11
  MALE                              39                              32
[1] 2 2
[1] FALSE
D16V8, binary
                                 cls
clus                               0  1
  DEL PEAK 16(13Q14.11) MUTATED   33 11
  DEL PEAK 16(13Q14.11) WILD-TYPE 29 13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(13Q14.11) MUTATED     33   11
  DEL PEAK 16(13Q14.11) WILD-TYPE   29   13
     clus
vv    DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE
  NO                             33                              29
  YES                            11                              13
[1] 2 2
[1] FALSE
D16V9, continuous
                                 vv
clus                              BIPHASIC MESOTHELIOMA
  DEL PEAK 16(13Q14.11) MUTATED                      11
  DEL PEAK 16(13Q14.11) WILD-TYPE                    12
                                 vv
clus                              DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK 16(13Q14.11) MUTATED                                      2
  DEL PEAK 16(13Q14.11) WILD-TYPE                                    3
                                 vv
clus                              EPITHELIOID MESOTHELIOMA
  DEL PEAK 16(13Q14.11) MUTATED                         30
  DEL PEAK 16(13Q14.11) WILD-TYPE                       27
                                 vv
clus                              SARCOMATOID MESOTHELIOMA
  DEL PEAK 16(13Q14.11) MUTATED                          1
  DEL PEAK 16(13Q14.11) WILD-TYPE                        1
D16V10, multiclass
                                      clus
vv                                     DEL PEAK 16(13Q14.11) MUTATED
  BIPHASIC MESOTHELIOMA                                           11
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                             2
  EPITHELIOID MESOTHELIOMA                                        30
  SARCOMATOID MESOTHELIOMA                                         1
                                      clus
vv                                     DEL PEAK 16(13Q14.11) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                             12
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                               3
  EPITHELIOID MESOTHELIOMA                                          27
  SARCOMATOID MESOTHELIOMA                                           1
[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                              R0 R1 R2 RX
  DEL PEAK 16(13Q14.11) MUTATED    7  2  6  7
  DEL PEAK 16(13Q14.11) WILD-TYPE 10  1  9  4
D16V11, multiclass
    clus
vv   DEL PEAK 16(13Q14.11) MUTATED DEL PEAK 16(13Q14.11) WILD-TYPE
  R0                             7                              10
  R1                             2                               1
  R2                             6                               9
  RX                             7                               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"

Clustering(17) Variable = DEL PEAK 17(14Q32.31) MUTATION ANALYSIS
D17V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 17(14Q32.31) MUTATED    3 35
  DEL PEAK 17(14Q32.31) WILD-TYPE  9 38
  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE 
                             38                              47 
  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE 
                             35                              38 
$`DEL PEAK 17(14Q32.31) MUTATED`
TCGA-3H-AB3S TCGA-3H-AB3L TCGA-3H-AB3M TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98I 
       12.66        11.87        29.10        48.99         4.67        28.27 
TCGA-3U-A98J TCGA-LK-A4NY TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 TCGA-LK-A4O6 
       24.36         5.52         6.08         1.87        12.72        14.73 
TCGA-LK-A4O7 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-SC-A6LN 
       11.51        18.81        23.31        77.56        19.99        13.61 
TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU TCGA-TS-A7OY 
        9.76        23.90         7.99        14.76        24.07         8.38 
TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A7P8 TCGA-TS-A8AF TCGA-TS-A8AY 
       27.75        41.46         9.30        15.02        11.77        15.42 
TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UD-AAC7 TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y 
        6.48         8.32        13.35        14.27         2.50         4.73 
TCGA-YS-A95B TCGA-ZN-A9VS 
        1.28        40.37 

$`DEL PEAK 17(14Q32.31) WILD-TYPE`
TCGA-3H-AB3O TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z TCGA-TS-A8AS 
       42.81        62.99        20.71        31.20        21.83        26.14 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3U-A98F 
       23.64        27.06        56.38        13.61        27.16        17.62 
TCGA-3U-A98H TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LM 
       38.01        17.95         8.02        80.84        91.73         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BR TCGA-NQ-A57I 
       17.33         3.52        10.95        24.89        68.71         0.66 
TCGA-SC-A6LM TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SH-A7BD TCGA-TS-A7OU TCGA-TS-A7P1 
       28.96         2.56        38.40        15.09        55.07        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7PB TCGA-TS-A8AI TCGA-UD-AABY TCGA-UD-AAC1 
       22.65        19.43        32.28        10.78        27.72        25.94 
TCGA-UD-AAC6 TCGA-UT-A88C TCGA-XT-AASU TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO 
       14.99        28.37         4.67         4.37         2.76         8.58 
TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
        7.50        16.41        32.12        43.04         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 
                          77.56                           91.73 
  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE 
                          13.48                           21.83 
[1] "1.3 - 77.6 (13.5)" "0.7 - 91.7 (21.8)"
[1] "hr=" "1.8"
D17V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 17(14Q32.31) MUTATED         3        1        0        8        23
  DEL PEAK 17(14Q32.31) WILD-TYPE       4        1        1        8        22
                                 vv
clus                              STAGE IV
  DEL PEAK 17(14Q32.31) MUTATED          4
  DEL PEAK 17(14Q32.31) WILD-TYPE       12
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                            23                              22
  STAGE IV                              4                              12
[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 12 18  3
  DEL PEAK 17(14Q32.31) WILD-TYPE 10 14 14 10
D17V4, multiclass
    clus
vv   DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE
  T1                             4                              10
  T2                            12                              14
  T3                            18                              14
  T4                             3                              10
[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    13
  DEL PEAK 17(14Q32.31) WILD-TYPE 25  4    16
D17V5, multiclass
       clus
vv      DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE
  N0                               19                              25
  N1                                6                               4
  N2+N3                            13                              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"
D17V6, binary
                                 cls
clus                               0  1
  DEL PEAK 17(14Q32.31) MUTATED   29  0
  DEL PEAK 17(14Q32.31) WILD-TYPE 28  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(14Q32.31) MUTATED     29    0
  DEL PEAK 17(14Q32.31) WILD-TYPE   28    3
   clus
vv  DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE
  0                            29                              28
  1                             0                               3
[1] 2 2
[1] FALSE
D17V7, binary
                                 cls
clus                               0  1
  DEL PEAK 17(14Q32.31) MUTATED   11 28
  DEL PEAK 17(14Q32.31) WILD-TYPE  5 43
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(14Q32.31) MUTATED     11   28
  DEL PEAK 17(14Q32.31) WILD-TYPE    5   43
        clus
vv       DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE
  FEMALE                            11                               5
  MALE                              28                              43
[1] 2 2
[1] FALSE
D17V8, binary
                                 cls
clus                               0  1
  DEL PEAK 17(14Q32.31) MUTATED   27 11
  DEL PEAK 17(14Q32.31) WILD-TYPE 35 13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(14Q32.31) MUTATED     27   11
  DEL PEAK 17(14Q32.31) WILD-TYPE   35   13
     clus
vv    DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE
  NO                             27                              35
  YES                            11                              13
[1] 2 2
[1] FALSE
D17V9, continuous
                                 vv
clus                              BIPHASIC MESOTHELIOMA
  DEL PEAK 17(14Q32.31) MUTATED                       7
  DEL PEAK 17(14Q32.31) WILD-TYPE                    16
                                 vv
clus                              DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK 17(14Q32.31) MUTATED                                      0
  DEL PEAK 17(14Q32.31) WILD-TYPE                                    5
                                 vv
clus                              EPITHELIOID MESOTHELIOMA
  DEL PEAK 17(14Q32.31) MUTATED                         31
  DEL PEAK 17(14Q32.31) WILD-TYPE                       26
                                 vv
clus                              SARCOMATOID MESOTHELIOMA
  DEL PEAK 17(14Q32.31) MUTATED                          1
  DEL PEAK 17(14Q32.31) WILD-TYPE                        1
D17V10, multiclass
                                      clus
vv                                     DEL PEAK 17(14Q32.31) MUTATED
  BIPHASIC MESOTHELIOMA                                            7
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                             0
  EPITHELIOID MESOTHELIOMA                                        31
  SARCOMATOID MESOTHELIOMA                                         1
                                      clus
vv                                     DEL PEAK 17(14Q32.31) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                             16
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                               5
  EPITHELIOID MESOTHELIOMA                                          26
  SARCOMATOID MESOTHELIOMA                                           1
[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                              R0 R1 R2 RX
  DEL PEAK 17(14Q32.31) MUTATED    7  3  5  7
  DEL PEAK 17(14Q32.31) WILD-TYPE 10  0 10  4
D17V11, multiclass
    clus
vv   DEL PEAK 17(14Q32.31) MUTATED DEL PEAK 17(14Q32.31) WILD-TYPE
  R0                             7                              10
  R1                             3                               0
  R2                             5                              10
  RX                             7                               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"

Clustering(18) Variable = DEL PEAK 18(15Q15.1) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(15Q15.1) MUTATED    1 26
  DEL PEAK 18(15Q15.1) WILD-TYPE 11 47
  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE 
                            27                             58 
  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE 
                            26                             47 
$`DEL PEAK 18(15Q15.1) MUTATED`
TCGA-3H-AB3S TCGA-3H-AB3M TCGA-3H-AB3T TCGA-3U-A98D TCGA-3U-A98F TCGA-LK-A4NY 
       12.66        29.10        13.61         4.67        17.62         5.52 
TCGA-LK-A4O0 TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BS 
        6.08        23.31        17.33         3.52        24.89        19.99 
TCGA-NQ-A57I TCGA-SC-A6LN TCGA-SH-A7BC TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU 
        0.66        13.61        23.90         7.99        14.76        24.07 
TCGA-TS-A7P0 TCGA-TS-A7P6 TCGA-TS-A8AF TCGA-UD-AABY TCGA-UD-AABZ TCGA-XT-AASU 
       41.46         9.30        11.77        27.72         6.48         4.67 
TCGA-YS-A95B TCGA-ZN-A9VO TCGA-ZN-A9VW 
        1.28         8.58         2.76 

$`DEL PEAK 18(15Q15.1) WILD-TYPE`
TCGA-3H-AB3O TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z TCGA-TS-A8AS 
       42.81        62.99        20.71        31.20        21.83        26.14 
TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3U TCGA-3H-AB3X 
       23.64        27.06        56.38        11.87        27.16        48.99 
TCGA-3U-A98H TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NZ TCGA-LK-A4O2 
       38.01        28.27        24.36        17.95         8.02         1.87 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LM TCGA-MQ-A6BL TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-SC-A6LM TCGA-SC-A6LP 
        5.19        10.95        77.56        68.71        28.96         2.56 
TCGA-SC-A6LQ TCGA-SC-A6LR TCGA-SH-A7BD TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ 
        9.76        38.40        15.09        55.07         8.38        27.75 
TCGA-TS-A7P1 TCGA-TS-A7P3 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AI 
       18.51        22.65        19.43        15.02        32.28        10.78 
TCGA-TS-A8AY TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
       15.42        25.94         8.32        14.99        13.35        28.37 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VP 
       14.27         2.50         4.73         4.37         2.76         7.50 
TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV 
       16.41        40.37        32.12        43.04 

  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE 
                          0.66                           1.87 
  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 
                         12.66                          20.07 
[1] "0.7 - 41.5 (12.7)" "1.9 - 91.7 (20.1)"
[1] "hr=" "2.3"
D18V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 18(15Q15.1) MUTATED         1        1        1        5        16
  DEL PEAK 18(15Q15.1) WILD-TYPE       6        1        0       11        29
                                vv
clus                             STAGE IV
  DEL PEAK 18(15Q15.1) MUTATED          4
  DEL PEAK 18(15Q15.1) WILD-TYPE       12
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                           16                             29
  STAGE IV                             4                             12
[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 10 11  4
  DEL PEAK 18(15Q15.1) WILD-TYPE 11 16 21  9
D18V4, multiclass
    clus
vv   DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE
  T1                            3                             11
  T2                           10                             16
  T3                           11                             21
  T4                            4                              9
[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   14  2     9
  DEL PEAK 18(15Q15.1) WILD-TYPE 30  8    20
D18V5, multiclass
       clus
vv      DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE
  N0                              14                             30
  N1                               2                              8
  N2+N3                            9                             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"
D18V6, binary
                                cls
clus                              0  1
  DEL PEAK 18(15Q15.1) MUTATED   19  1
  DEL PEAK 18(15Q15.1) WILD-TYPE 38  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(15Q15.1) MUTATED     19    1
  DEL PEAK 18(15Q15.1) WILD-TYPE   38    2
   clus
vv  DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE
  0                           19                             38
  1                            1                              2
[1] 2 2
[1] FALSE
D18V7, binary
                                cls
clus                              0  1
  DEL PEAK 18(15Q15.1) MUTATED    5 23
  DEL PEAK 18(15Q15.1) WILD-TYPE 11 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(15Q15.1) MUTATED      5   23
  DEL PEAK 18(15Q15.1) WILD-TYPE   11   48
        clus
vv       DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE
  FEMALE                            5                             11
  MALE                             23                             48
[1] 2 2
[1] FALSE
D18V8, binary
                                cls
clus                              0  1
  DEL PEAK 18(15Q15.1) MUTATED   19  8
  DEL PEAK 18(15Q15.1) WILD-TYPE 43 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(15Q15.1) MUTATED     19    8
  DEL PEAK 18(15Q15.1) WILD-TYPE   43   16
     clus
vv    DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE
  NO                            19                             43
  YES                            8                             16
[1] 2 2
[1] FALSE
D18V9, continuous
                                vv
clus                             BIPHASIC MESOTHELIOMA
  DEL PEAK 18(15Q15.1) MUTATED                      11
  DEL PEAK 18(15Q15.1) WILD-TYPE                    12
                                vv
clus                             DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK 18(15Q15.1) MUTATED                                      1
  DEL PEAK 18(15Q15.1) WILD-TYPE                                    4
                                vv
clus                             EPITHELIOID MESOTHELIOMA
  DEL PEAK 18(15Q15.1) MUTATED                         15
  DEL PEAK 18(15Q15.1) WILD-TYPE                       42
                                vv
clus                             SARCOMATOID MESOTHELIOMA
  DEL PEAK 18(15Q15.1) MUTATED                          1
  DEL PEAK 18(15Q15.1) WILD-TYPE                        1
D18V10, multiclass
                                      clus
vv                                     DEL PEAK 18(15Q15.1) MUTATED
  BIPHASIC MESOTHELIOMA                                          11
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                            1
  EPITHELIOID MESOTHELIOMA                                       15
  SARCOMATOID MESOTHELIOMA                                        1
                                      clus
vv                                     DEL PEAK 18(15Q15.1) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                            12
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                              4
  EPITHELIOID MESOTHELIOMA                                         42
  SARCOMATOID MESOTHELIOMA                                          1
[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                             R0 R1 R2 RX
  DEL PEAK 18(15Q15.1) MUTATED    8  0  4  3
  DEL PEAK 18(15Q15.1) WILD-TYPE  9  3 11  8
D18V11, multiclass
    clus
vv   DEL PEAK 18(15Q15.1) MUTATED DEL PEAK 18(15Q15.1) WILD-TYPE
  R0                            8                              9
  R1                            0                              3
  R2                            4                             11
  RX                            3                              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"

Clustering(19) Variable = DEL PEAK 19(16P13.3) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 19(16P13.3) MUTATED    2  4
  DEL PEAK 19(16P13.3) WILD-TYPE 10 69
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                             6                             79 
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                             4                             69 
$`DEL PEAK 19(16P13.3) MUTATED`
TCGA-LK-A4O0 TCGA-MQ-A4LM TCGA-MQ-A6BR TCGA-UT-A88G TCGA-UT-A97Y TCGA-ZN-A9VV 
        6.08         5.19        68.71         2.50         4.73        43.04 

$`DEL PEAK 19(16P13.3) WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3T TCGA-3H-AB3U TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H 
       13.61        27.16        48.99         4.67        17.62        38.01 
TCGA-3U-A98I TCGA-3U-A98J TCGA-LK-A4NW TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O2 
       28.27        24.36        17.95         5.52         8.02         1.87 
TCGA-LK-A4O5 TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LI 
       12.72        14.73        11.51        80.84        91.73        18.81 
TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BL TCGA-MQ-A6BN TCGA-MQ-A6BQ 
       23.31        17.33         3.52        10.95        24.89        77.56 
TCGA-MQ-A6BS TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LP TCGA-SC-A6LQ 
       19.99         0.66        28.96        13.61         2.56         9.76 
TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT TCGA-SH-A9CU 
       38.40        23.90        15.09         7.99        14.76        24.07 
TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       55.07         8.38        27.75        41.46        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
        9.30        19.43        15.02        32.28        11.77        10.78 
TCGA-TS-A8AY TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 
       15.42        27.72         6.48        25.94         8.32        14.99 
TCGA-UD-AAC7 TCGA-UT-A88C TCGA-UT-A88E TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       13.35        28.37        14.27         4.67         1.28         4.37 
TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU 
        2.76         8.58         7.50        16.41        40.37        32.12 
TCGA-ZN-A9VW 
        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 
                         68.71                          91.73 
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                         5.635                         17.620 
[1] "2.5 - 68.7 (5.6)"  "0.7 - 91.7 (17.6)"
[1] "hr=" "1.2"
D19V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 19(16P13.3) MUTATED         1        1        0        0         4
  DEL PEAK 19(16P13.3) WILD-TYPE       6        1        1       16        41
                                vv
clus                             STAGE IV
  DEL PEAK 19(16P13.3) MUTATED          0
  DEL PEAK 19(16P13.3) WILD-TYPE       16
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                            4                             41
  STAGE IV                             0                             16
[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  3  0
  DEL PEAK 19(16P13.3) WILD-TYPE 11 26 29 13
D19V4, multiclass
    clus
vv   DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  T1                            3                             11
  T2                            0                             26
  T3                            3                             29
  T4                            0                             13
[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     1
  DEL PEAK 19(16P13.3) WILD-TYPE 40  9    28
D19V5, multiclass
       clus
vv      DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  N0                               4                             40
  N1                               1                              9
  N2+N3                            1                             28
[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 53  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(16P13.3) MUTATED      4    0
  DEL PEAK 19(16P13.3) WILD-TYPE   53    3
   clus
vv  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  0                            4                             53
  1                            0                              3
[1] 2 2
[1] FALSE
D19V7, binary
                                cls
clus                              0  1
  DEL PEAK 19(16P13.3) MUTATED    2  4
  DEL PEAK 19(16P13.3) WILD-TYPE 14 67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(16P13.3) MUTATED      2    4
  DEL PEAK 19(16P13.3) WILD-TYPE   14   67
        clus
vv       DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  FEMALE                            2                             14
  MALE                              4                             67
[1] 2 2
[1] FALSE
D19V8, binary
                                cls
clus                              0  1
  DEL PEAK 19(16P13.3) MUTATED    5  1
  DEL PEAK 19(16P13.3) WILD-TYPE 57 23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(16P13.3) MUTATED      5    1
  DEL PEAK 19(16P13.3) WILD-TYPE   57   23
     clus
vv    DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  NO                             5                             57
  YES                            1                             23
[1] 2 2
[1] FALSE
D19V9, continuous
                                vv
clus                             BIPHASIC MESOTHELIOMA
  DEL PEAK 19(16P13.3) MUTATED                       3
  DEL PEAK 19(16P13.3) WILD-TYPE                    20
                                vv
clus                             DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK 19(16P13.3) MUTATED                                      0
  DEL PEAK 19(16P13.3) WILD-TYPE                                    5
                                vv
clus                             EPITHELIOID MESOTHELIOMA
  DEL PEAK 19(16P13.3) MUTATED                          2
  DEL PEAK 19(16P13.3) WILD-TYPE                       55
                                vv
clus                             SARCOMATOID MESOTHELIOMA
  DEL PEAK 19(16P13.3) MUTATED                          1
  DEL PEAK 19(16P13.3) WILD-TYPE                        1
D19V10, multiclass
                                      clus
vv                                     DEL PEAK 19(16P13.3) MUTATED
  BIPHASIC MESOTHELIOMA                                           3
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                            0
  EPITHELIOID MESOTHELIOMA                                        2
  SARCOMATOID MESOTHELIOMA                                        1
                                      clus
vv                                     DEL PEAK 19(16P13.3) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                            20
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                              5
  EPITHELIOID MESOTHELIOMA                                         55
  SARCOMATOID MESOTHELIOMA                                          1
[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                             R0 R1 R2 RX
  DEL PEAK 19(16P13.3) MUTATED    1  0  0  3
  DEL PEAK 19(16P13.3) WILD-TYPE 16  3 15  8
D19V11, multiclass
    clus
vv   DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  R0                            1                             16
  R1                            0                              3
  R2                            0                             15
  RX                            3                              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"

Clustering(20) Variable = DEL PEAK 20(16Q24.1) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 20(16Q24.1) MUTATED    2 19
  DEL PEAK 20(16Q24.1) WILD-TYPE 10 54
  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE 
                            21                             64 
  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE 
                            19                             54 
$`DEL PEAK 20(16Q24.1) MUTATED`
TCGA-3H-AB3T TCGA-3H-AB3X TCGA-3U-A98F TCGA-3U-A98I TCGA-LK-A4NW TCGA-LK-A4NY 
       13.61        48.99        17.62        28.27        17.95         5.52 
TCGA-LK-A4O0 TCGA-LK-A4O6 TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LP TCGA-MQ-A4LV 
        6.08        14.73        18.81        23.31        17.33         3.52 
TCGA-MQ-A6BS TCGA-SC-A6LQ TCGA-TS-A8AY TCGA-UD-AABZ TCGA-UD-AAC7 TCGA-UT-A88G 
       19.99         9.76        15.42         6.48        13.35         2.50 
TCGA-UT-A97Y TCGA-YS-A95B TCGA-ZN-A9VQ 
        4.73         1.28        16.41 

$`DEL PEAK 20(16Q24.1) WILD-TYPE`
TCGA-3H-AB3O TCGA-3H-AB3S TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z 
       42.81        12.66        62.99        20.71        31.20        21.83 
TCGA-TS-A8AS TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       26.14        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3U TCGA-3U-A98D TCGA-3U-A98H TCGA-3U-A98J TCGA-LK-A4NZ TCGA-LK-A4O2 
       27.16         4.67        38.01        24.36         8.02         1.87 
TCGA-LK-A4O5 TCGA-LK-A4O7 TCGA-MQ-A4KX TCGA-MQ-A4LC TCGA-MQ-A4LM TCGA-MQ-A6BL 
       12.72        11.51        80.84        91.73         5.19        10.95 
TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BR TCGA-NQ-A57I TCGA-SC-A6LM TCGA-SC-A6LN 
       24.89        77.56        68.71         0.66        28.96        13.61 
TCGA-SC-A6LP TCGA-SC-A6LR TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A7BH TCGA-SH-A9CT 
        2.56        38.40        23.90        15.09         7.99        14.76 
TCGA-SH-A9CU TCGA-TS-A7OU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 
       24.07        55.07         8.38        27.75        41.46        18.51 
TCGA-TS-A7P3 TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF 
       22.65         9.30        19.43        15.02        32.28        11.77 
TCGA-TS-A8AI TCGA-UD-AABY TCGA-UD-AAC1 TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UT-A88C 
       10.78        27.72        25.94         8.32        14.99        28.37 
TCGA-UT-A88E TCGA-XT-AASU TCGA-YS-A95C TCGA-YS-AA4M TCGA-ZN-A9VO TCGA-ZN-A9VP 
       14.27         4.67         4.37         2.76         8.58         7.50 
TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV TCGA-ZN-A9VW 
       40.37        32.12        43.04         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 
                         48.99                          91.73 
  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE 
                         14.73                          21.27 
[1] "1.3 - 49.0 (14.7)" "0.7 - 91.7 (21.3)"
[1] "hr=" "2"  
D20V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 20(16Q24.1) MUTATED         3        1        0        5        10
  DEL PEAK 20(16Q24.1) WILD-TYPE       4        1        1       11        35
                                vv
clus                             STAGE IV
  DEL PEAK 20(16Q24.1) MUTATED          3
  DEL PEAK 20(16Q24.1) WILD-TYPE       13
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                           10                             35
  STAGE IV                             3                             13
[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  9  3
  DEL PEAK 20(16Q24.1) WILD-TYPE 10 20 23 10
D20V4, multiclass
    clus
vv   DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE
  T1                            4                             10
  T2                            6                             20
  T3                            9                             23
  T4                            3                             10
[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   14  3     4
  DEL PEAK 20(16Q24.1) WILD-TYPE 30  7    25
D20V5, multiclass
       clus
vv      DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE
  N0                              14                             30
  N1                               3                              7
  N2+N3                            4                             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                                cls
clus                              0  1
  DEL PEAK 20(16Q24.1) MUTATED   19  0
  DEL PEAK 20(16Q24.1) WILD-TYPE 38  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(16Q24.1) MUTATED     19    0
  DEL PEAK 20(16Q24.1) WILD-TYPE   38    3
   clus
vv  DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE
  0                           19                             38
  1                            0                              3
[1] 2 2
[1] FALSE
D20V7, binary
                                cls
clus                              0  1
  DEL PEAK 20(16Q24.1) MUTATED    7 15
  DEL PEAK 20(16Q24.1) WILD-TYPE  9 56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(16Q24.1) MUTATED      7   15
  DEL PEAK 20(16Q24.1) WILD-TYPE    9   56
        clus
vv       DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE
  FEMALE                            7                              9
  MALE                             15                             56
[1] 2 2
[1] FALSE
D20V8, binary
                                cls
clus                              0  1
  DEL PEAK 20(16Q24.1) MUTATED   14  7
  DEL PEAK 20(16Q24.1) WILD-TYPE 48 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(16Q24.1) MUTATED     14    7
  DEL PEAK 20(16Q24.1) WILD-TYPE   48   17
     clus
vv    DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE
  NO                            14                             48
  YES                            7                             17
[1] 2 2
[1] FALSE
D20V9, 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                             16 
                    TCGA-3U-A98E                     TCGA-UT-A88D 
"DEL PEAK 20(16Q24.1) WILD-TYPE" "DEL PEAK 20(16Q24.1) WILD-TYPE" 
                    TCGA-3U-A98J                     TCGA-SC-A6LM 
"DEL PEAK 20(16Q24.1) WILD-TYPE" "DEL PEAK 20(16Q24.1) WILD-TYPE" 
                    TCGA-SC-A6LN                     TCGA-SC-A6LP 
"DEL PEAK 20(16Q24.1) WILD-TYPE" "DEL PEAK 20(16Q24.1) WILD-TYPE" 
                    TCGA-SC-A6LR                     TCGA-SH-A7BH 
"DEL PEAK 20(16Q24.1) WILD-TYPE" "DEL PEAK 20(16Q24.1) WILD-TYPE" 
                    TCGA-SH-A9CT                     TCGA-SH-A9CU 
"DEL PEAK 20(16Q24.1) WILD-TYPE" "DEL PEAK 20(16Q24.1) WILD-TYPE" 
                    TCGA-UT-A88C                     TCGA-XT-AASU 
"DEL PEAK 20(16Q24.1) WILD-TYPE" "DEL PEAK 20(16Q24.1) WILD-TYPE" 
                    TCGA-ZN-A9VO                     TCGA-ZN-A9VP 
"DEL PEAK 20(16Q24.1) WILD-TYPE" "DEL PEAK 20(16Q24.1) WILD-TYPE" 
                    TCGA-ZN-A9VS                     TCGA-ZN-A9VU 
"DEL PEAK 20(16Q24.1) WILD-TYPE" "DEL PEAK 20(16Q24.1) WILD-TYPE" 
                                vv
clus                             BIPHASIC MESOTHELIOMA
  DEL PEAK 20(16Q24.1) MUTATED                       9
  DEL PEAK 20(16Q24.1) WILD-TYPE                    14
                                vv
clus                             DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK 20(16Q24.1) MUTATED                                      1
  DEL PEAK 20(16Q24.1) WILD-TYPE                                    4
                                vv
clus                             EPITHELIOID MESOTHELIOMA
  DEL PEAK 20(16Q24.1) MUTATED                         11
  DEL PEAK 20(16Q24.1) WILD-TYPE                       46
                                vv
clus                             SARCOMATOID MESOTHELIOMA
  DEL PEAK 20(16Q24.1) MUTATED                          1
  DEL PEAK 20(16Q24.1) WILD-TYPE                        1
D20V10, multiclass
                                      clus
vv                                     DEL PEAK 20(16Q24.1) MUTATED
  BIPHASIC MESOTHELIOMA                                           9
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                            1
  EPITHELIOID MESOTHELIOMA                                       11
  SARCOMATOID MESOTHELIOMA                                        1
                                      clus
vv                                     DEL PEAK 20(16Q24.1) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                            14
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                              4
  EPITHELIOID MESOTHELIOMA                                         46
  SARCOMATOID MESOTHELIOMA                                          1
[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                             R0 R1 R2 RX
  DEL PEAK 20(16Q24.1) MUTATED    6  1  2  5
  DEL PEAK 20(16Q24.1) WILD-TYPE 11  2 13  6
D20V11, multiclass
    clus
vv   DEL PEAK 20(16Q24.1) MUTATED DEL PEAK 20(16Q24.1) WILD-TYPE
  R0                            6                             11
  R1                            1                              2
  R2                            2                             13
  RX                            5                              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"

Clustering(21) Variable = DEL PEAK 21(22Q12.2) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 21(22Q12.2) MUTATED    8 59
  DEL PEAK 21(22Q12.2) WILD-TYPE  4 14
  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE 
                            67                             18 
  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE 
                            59                             14 
$`DEL PEAK 21(22Q12.2) MUTATED`
TCGA-3H-AB3S TCGA-UD-AAC4 TCGA-UT-A88D TCGA-3H-AB3K TCGA-3H-AB3L TCGA-3H-AB3M 
       12.66        23.64        27.06        56.38        11.87        29.10 
TCGA-3H-AB3T TCGA-3H-AB3X TCGA-3U-A98D TCGA-3U-A98F TCGA-3U-A98H TCGA-3U-A98I 
       13.61        48.99         4.67        17.62        38.01        28.27 
TCGA-3U-A98J TCGA-LK-A4NY TCGA-LK-A4NZ TCGA-LK-A4O0 TCGA-LK-A4O2 TCGA-LK-A4O5 
       24.36         5.52         8.02         6.08         1.87        12.72 
TCGA-LK-A4O6 TCGA-LK-A4O7 TCGA-MQ-A4LC TCGA-MQ-A4LI TCGA-MQ-A4LJ TCGA-MQ-A4LM 
       14.73        11.51        91.73        18.81        23.31         5.19 
TCGA-MQ-A4LP TCGA-MQ-A4LV TCGA-MQ-A6BN TCGA-MQ-A6BQ TCGA-MQ-A6BS TCGA-NQ-A57I 
       17.33         3.52        24.89        77.56        19.99         0.66 
TCGA-SC-A6LM TCGA-SC-A6LN TCGA-SC-A6LQ TCGA-SH-A7BC TCGA-SH-A7BD TCGA-SH-A9CT 
       28.96        13.61         9.76        23.90        15.09        14.76 
TCGA-SH-A9CU TCGA-TS-A7OY TCGA-TS-A7OZ TCGA-TS-A7P0 TCGA-TS-A7P1 TCGA-TS-A7P3 
       24.07         8.38        27.75        41.46        18.51        22.65 
TCGA-TS-A7P6 TCGA-TS-A7P7 TCGA-TS-A7P8 TCGA-TS-A7PB TCGA-TS-A8AF TCGA-TS-A8AI 
        9.30        19.43        15.02        32.28        11.77        10.78 
TCGA-UD-AABY TCGA-UD-AABZ TCGA-UD-AAC5 TCGA-UD-AAC6 TCGA-UD-AAC7 TCGA-UT-A88C 
       27.72         6.48         8.32        14.99        13.35        28.37 
TCGA-UT-A88E TCGA-UT-A88G TCGA-UT-A97Y TCGA-XT-AASU TCGA-YS-A95B TCGA-YS-A95C 
       14.27         2.50         4.73         4.67         1.28         4.37 
TCGA-ZN-A9VO TCGA-ZN-A9VP TCGA-ZN-A9VQ TCGA-ZN-A9VS TCGA-ZN-A9VU TCGA-ZN-A9VV 
        8.58         7.50        16.41        40.37        32.12        43.04 
TCGA-ZN-A9VW 
        2.76 

$`DEL PEAK 21(22Q12.2) WILD-TYPE`
TCGA-3H-AB3O TCGA-3U-A98E TCGA-3U-A98G TCGA-LK-A4O4 TCGA-SC-AA5Z TCGA-TS-A8AS 
       42.81        62.99        20.71        31.20        21.83        26.14 
TCGA-3H-AB3U TCGA-LK-A4NW TCGA-MQ-A4KX TCGA-MQ-A6BL TCGA-MQ-A6BR TCGA-SC-A6LP 
       27.16        17.95        80.84        10.95        68.71         2.56 
TCGA-SC-A6LR TCGA-SH-A7BH TCGA-TS-A7OU TCGA-TS-A8AY TCGA-UD-AAC1 TCGA-YS-AA4M 
       38.40         7.99        55.07        15.42        25.94         2.76 

  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE 
                          0.66                           2.56 
  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 
                         14.99                          26.04 
[1] "0.7 - 91.7 (15.0)" "2.6 - 80.8 (26.0)"
[1] "hr=" "1.8"
D21V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE III
  DEL PEAK 21(22Q12.2) MUTATED         6        1        1       14        36
  DEL PEAK 21(22Q12.2) WILD-TYPE       1        1        0        2         9
                                vv
clus                             STAGE IV
  DEL PEAK 21(22Q12.2) MUTATED         10
  DEL PEAK 21(22Q12.2) WILD-TYPE        6
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                           36                              9
  STAGE IV                            10                              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 21(22Q12.2) MUTATED    9 21 28  8
  DEL PEAK 21(22Q12.2) WILD-TYPE  5  5  4  5
D21V4, multiclass
    clus
vv   DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE
  T1                            9                              5
  T2                           21                              5
  T3                           28                              4
  T4                            8                              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 21(22Q12.2) MUTATED   34  7    23
  DEL PEAK 21(22Q12.2) WILD-TYPE 10  3     6
D21V5, multiclass
       clus
vv      DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE
  N0                              34                             10
  N1                               7                              3
  N2+N3                           23                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                                cls
clus                              0  1
  DEL PEAK 21(22Q12.2) MUTATED   44  2
  DEL PEAK 21(22Q12.2) WILD-TYPE 13  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(22Q12.2) MUTATED     44    2
  DEL PEAK 21(22Q12.2) WILD-TYPE   13    1
   clus
vv  DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE
  0                           44                             13
  1                            2                              1
[1] 2 2
[1] FALSE
D21V7, binary
                                cls
clus                              0  1
  DEL PEAK 21(22Q12.2) MUTATED   11 57
  DEL PEAK 21(22Q12.2) WILD-TYPE  5 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(22Q12.2) MUTATED     11   57
  DEL PEAK 21(22Q12.2) WILD-TYPE    5   14
        clus
vv       DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE
  FEMALE                           11                              5
  MALE                             57                             14
[1] 2 2
[1] FALSE
D21V8, binary
                                cls
clus                              0  1
  DEL PEAK 21(22Q12.2) MUTATED   47 20
  DEL PEAK 21(22Q12.2) WILD-TYPE 15  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(22Q12.2) MUTATED     47   20
  DEL PEAK 21(22Q12.2) WILD-TYPE   15    4
     clus
vv    DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE
  NO                            47                             15
  YES                           20                              4
[1] 2 2
[1] FALSE
D21V9, continuous
                                vv
clus                             BIPHASIC MESOTHELIOMA
  DEL PEAK 21(22Q12.2) MUTATED                      19
  DEL PEAK 21(22Q12.2) WILD-TYPE                     4
                                vv
clus                             DIFFUSE MALIGNANT MESOTHELIOMA - NOS
  DEL PEAK 21(22Q12.2) MUTATED                                      3
  DEL PEAK 21(22Q12.2) WILD-TYPE                                    2
                                vv
clus                             EPITHELIOID MESOTHELIOMA
  DEL PEAK 21(22Q12.2) MUTATED                         45
  DEL PEAK 21(22Q12.2) WILD-TYPE                       12
                                vv
clus                             SARCOMATOID MESOTHELIOMA
  DEL PEAK 21(22Q12.2) MUTATED                          1
  DEL PEAK 21(22Q12.2) WILD-TYPE                        1
D21V10, multiclass
                                      clus
vv                                     DEL PEAK 21(22Q12.2) MUTATED
  BIPHASIC MESOTHELIOMA                                          19
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                            3
  EPITHELIOID MESOTHELIOMA                                       45
  SARCOMATOID MESOTHELIOMA                                        1
                                      clus
vv                                     DEL PEAK 21(22Q12.2) WILD-TYPE
  BIPHASIC MESOTHELIOMA                                             4
  DIFFUSE MALIGNANT MESOTHELIOMA - NOS                              2
  EPITHELIOID MESOTHELIOMA                                         12
  SARCOMATOID MESOTHELIOMA                                          1
[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                             R0 R1 R2 RX
  DEL PEAK 21(22Q12.2) MUTATED   14  3 10  8
  DEL PEAK 21(22Q12.2) WILD-TYPE  3  0  5  3
D21V11, multiclass
    clus
vv   DEL PEAK 21(22Q12.2) MUTATED DEL PEAK 21(22Q12.2) WILD-TYPE
  R0                           14                              3
  R1                            3                              0
  R2                           10                              5
  RX                            8                              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"
