[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTKIRP-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/KIRP-TP/10005964/KIRP-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/10013765/transformed.cor.cli.txt"

nPatients in clinical file=202, in cluster file=224, common to both=198
[1]  29 198
[1] "AMP PEAK 1(2P23.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                          39                          159 
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                          39                          159 
[1] "AMP PEAK 2(2Q32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                          45                          153 
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                          45                          153 
[1] "AMP PEAK 3(3P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 3(3P12.1) MUTATED AMP PEAK 3(3P12.1) WILD-TYPE 
                          59                          139 
  AMP PEAK 3(3P12.1) MUTATED AMP PEAK 3(3P12.1) WILD-TYPE 
                          59                          139 
[1] "AMP PEAK 4(3Q26.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 4(3Q26.31) MUTATED AMP PEAK 4(3Q26.31) WILD-TYPE 
                           73                           125 
  AMP PEAK 4(3Q26.31) MUTATED AMP PEAK 4(3Q26.31) WILD-TYPE 
                           73                           125 
[1] "AMP PEAK 5(7Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE 
                         122                           76 
  AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE 
                         122                           76 
[1] "AMP PEAK 6(17Q25.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                          145                            53 
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                          145                            53 
[1] "AMP PEAK 7(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                           22                           176 
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                           22                           176 
[1] "DEL PEAK  1(1P36.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            39                            159 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            39                            159 
[1] "DEL PEAK  2(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(2Q37.3) MUTATED DEL PEAK  2(2Q37.3) WILD-TYPE 
                            9                           189 
  DEL PEAK  2(2Q37.3) MUTATED DEL PEAK  2(2Q37.3) WILD-TYPE 
                            9                           189 
[1] "DEL PEAK  3(3P22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(3P22.1) MUTATED DEL PEAK  3(3P22.1) WILD-TYPE 
                           17                           181 
  DEL PEAK  3(3P22.1) MUTATED DEL PEAK  3(3P22.1) WILD-TYPE 
                           17                           181 
[1] "DEL PEAK  4(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE 
                           24                           174 
  DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE 
                           24                           174 
[1] "DEL PEAK  5(5P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(5P14.2) MUTATED DEL PEAK  5(5P14.2) WILD-TYPE 
                           10                           188 
  DEL PEAK  5(5P14.2) MUTATED DEL PEAK  5(5P14.2) WILD-TYPE 
                           10                           188 
[1] "DEL PEAK  6(5Q35.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE 
                           11                           187 
  DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE 
                           11                           187 
[1] "DEL PEAK  7(6P12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                           18                           180 
  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                           18                           180 
[1] "DEL PEAK  8(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(6Q22.31) MUTATED DEL PEAK  8(6Q22.31) WILD-TYPE 
                            20                            178 
  DEL PEAK  8(6Q22.31) MUTATED DEL PEAK  8(6Q22.31) WILD-TYPE 
                            20                            178 
[1] "DEL PEAK  9(6Q27) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE 
                         23                         175 
  DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE 
                         23                         175 
[1] "DEL PEAK 10(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                           29                           169 
  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                           29                           169 
[1] "DEL PEAK 11(10P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(10P11.21) MUTATED DEL PEAK 11(10P11.21) WILD-TYPE 
                             12                             186 
  DEL PEAK 11(10P11.21) MUTATED DEL PEAK 11(10P11.21) WILD-TYPE 
                             12                             186 
[1] "DEL PEAK 12(11Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(11Q22.3) MUTATED DEL PEAK 12(11Q22.3) WILD-TYPE 
                            20                            178 
  DEL PEAK 12(11Q22.3) MUTATED DEL PEAK 12(11Q22.3) WILD-TYPE 
                            20                            178 
[1] "DEL PEAK 13(11Q24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(11Q24.2) MUTATED DEL PEAK 13(11Q24.2) WILD-TYPE 
                            20                            178 
  DEL PEAK 13(11Q24.2) MUTATED DEL PEAK 13(11Q24.2) WILD-TYPE 
                            20                            178 
[1] "DEL PEAK 14(14Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(14Q11.2) MUTATED DEL PEAK 14(14Q11.2) WILD-TYPE 
                            40                            158 
  DEL PEAK 14(14Q11.2) MUTATED DEL PEAK 14(14Q11.2) WILD-TYPE 
                            40                            158 
[1] "DEL PEAK 15(15Q13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(15Q13.3) MUTATED DEL PEAK 15(15Q13.3) WILD-TYPE 
                            25                            173 
  DEL PEAK 15(15Q13.3) MUTATED DEL PEAK 15(15Q13.3) WILD-TYPE 
                            25                            173 
[1] "DEL PEAK 16(16Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(16Q24.1) MUTATED DEL PEAK 16(16Q24.1) WILD-TYPE 
                             9                            189 
  DEL PEAK 16(16Q24.1) MUTATED DEL PEAK 16(16Q24.1) WILD-TYPE 
                             9                            189 
[1] "DEL PEAK 17(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(19P13.3) MUTATED DEL PEAK 17(19P13.3) WILD-TYPE 
                            17                            181 
  DEL PEAK 17(19P13.3) MUTATED DEL PEAK 17(19P13.3) WILD-TYPE 
                            17                            181 
[1] "DEL PEAK 18(19Q13.42) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(19Q13.42) MUTATED DEL PEAK 18(19Q13.42) WILD-TYPE 
                             16                             182 
  DEL PEAK 18(19Q13.42) MUTATED DEL PEAK 18(19Q13.42) WILD-TYPE 
                             16                             182 
[1] "DEL PEAK 19(21Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(21Q22.3) MUTATED DEL PEAK 19(21Q22.3) WILD-TYPE 
                            33                            165 
  DEL PEAK 19(21Q22.3) MUTATED DEL PEAK 19(21Q22.3) WILD-TYPE 
                            33                            165 
[1] "DEL PEAK 20(22Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(22Q12.2) MUTATED DEL PEAK 20(22Q12.2) WILD-TYPE 
                            50                            148 
  DEL PEAK 20(22Q12.2) MUTATED DEL PEAK 20(22Q12.2) WILD-TYPE 
                            50                            148 
[1] "DEL PEAK 21(XP11.22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(XP11.22) MUTATED DEL PEAK 21(XP11.22) WILD-TYPE 
                            20                            178 
  DEL PEAK 21(XP11.22) MUTATED DEL PEAK 21(XP11.22) WILD-TYPE 
                            20                            178 
[1] "DEL PEAK 22(XQ28) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(XQ28) MUTATED DEL PEAK 22(XQ28) WILD-TYPE 
                         19                         179 
  DEL PEAK 22(XQ28) MUTATED DEL PEAK 22(XQ28) WILD-TYPE 
                         19                         179 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 198 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
         554           21          493            3           NA           NA 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
         582           27           NA            7           49            2 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
         140          780          729           NA          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
         597          600          436          379          516           NA 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-A4-A772 
          NA            2          118           87            4           NA 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
          NA         1778         1636          412          923          763 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
        1357           26           67          595          223          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
         747          108          510           14         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379           85         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
         671           64          585          207            5          102 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
         167           52         2639          586          270         1938 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
          NA           NA         1454           NA         1242          792 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
         921          792          771          403           NA          233 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
          29          364           NA           84         3760           NA 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        2948         2839           NA         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
         799          612           NA          232          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
         116          353          414         3950         1093         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          445           92         1240 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        2429         2460           NA         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
         578          757           97           10            7           36 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
         208         1575         1479           NA         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 
         765          446          786          279           NA         5925 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
         393          112          841           32          178           91 
TCGA-HE-7128 TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          NA           NA           NA         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
        1726          167          511          608           62          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD 
         649          146            2           NA            4          160 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          391          543          438 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         292           11          541          148         3035         2653 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
          NA           NA         2584         2816          391          174 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
          57         1079         1199          994          508          423 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS 
          NA          102          925           NA          494         1247 
TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         847          224            2          186          181          205 
Variable 1:'AGE':	nDistinctValues=51,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=161,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                         "NEOPLASM.DISEASESTAGE"      
 [3] "PATHOLOGY.T.STAGE"           "PATHOLOGY.N.STAGE"          
 [5] "PATHOLOGY.M.STAGE"           "GENDER"                     
 [7] "KARNOFSKY.PERFORMANCE.SCORE" "NUMBERPACKYEARSSMOKED"      
 [9] "RACE"                        "ETHNICITY"                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 198 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=51, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
130  18  48   2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  130    18    50 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
130  18  48   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  130    18    50 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
33 20  4 
[1] "table(vv)"
vv
N0 N1 N2 
33 20  4 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
33 20  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
33 20  4 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=15, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK 1(2P23.2) MUTATION ANALYSIS
D1V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 1(2P23.2) MUTATED    31   2
  AMP PEAK 1(2P23.2) WILD-TYPE 135   5
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                          33                          140 
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                           2                            5 
$`AMP PEAK 1(2P23.2) MUTATED`
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 
         516            2          118          412           67          223 
TCGA-B3-A6W5 TCGA-B9-4117 TCGA-B9-A44B TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7046 
          85           14           64          364           84         2948 
TCGA-DW-5561 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-A8LD 
         414           36          208         1575         1194         1967 
TCGA-GL-7966 TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-IA-A40U TCGA-IA-A40Y 
         112           91         2072          360          511           62 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5EB TCGA-PJ-A5Z9 
         160          885          161         1043         2584          174 
TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SQ 
          57          508          494 

$`AMP PEAK 1(2P23.2) WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 
          87            4         1778         1636          923          763 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
        1357           26          595          659          747          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
         510           14         1029          307          930         1049 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 
         379         1536          857          803          627           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
         460         1338          671          585          207            5 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         102          167           52         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7048 
         771          403          233           29         3760         2839 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
        1864         1533         1516          799          612          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 
         214          218          116          353         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1240         2429         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6792 
         578          757           97           10            7         1479 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
        1059          765          446          786          279         5925 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-HE-A5NH TCGA-HE-A5NJ 
         393          841           32          178          408         1726 
TCGA-HE-A5NL TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         167          608          677          649          146            2 
TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
           4          391          543          438          292           11 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 
         541          148         3035         2653         2816          391 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1079         1199          994          423         1973          102 
TCGA-SX-A7SO TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
         925         1247          847          224            2          186 
TCGA-Y8-A898 TCGA-Y8-A8RZ 
         181          205 

  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                           2                            2 
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                        2948                         5925 
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                       223.0                        583.5 
[1] "2.0 - 2948.0 (223.0)" "2.0 - 5925.0 (583.5)"
[1] "hr=" "1.7"
D1V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 1(2P23.2) MUTATED        23        2         8        5
  AMP PEAK 1(2P23.2) WILD-TYPE      99        9        34        7
D1V3, multiclass
           clus
vv          AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE
  STAGE I                           23                           99
  STAGE II                           2                            9
  STAGE III                          8                           34
  STAGE IV                           5                            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                            T1  T2 T3+T4
  AMP PEAK 1(2P23.2) MUTATED    23   4    12
  AMP PEAK 1(2P23.2) WILD-TYPE 107  14    38
D1V4, multiclass
       clus
vv      AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE
  T1                            23                          107
  T2                             4                           14
  T3+T4                         12                           38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2
  AMP PEAK 1(2P23.2) MUTATED    4  8  1
  AMP PEAK 1(2P23.2) WILD-TYPE 29 12  3
D1V5, multiclass
    clus
vv   AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE
  N0                          4                           29
  N1                          8                           12
  N2                          1                            3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1 MX
  AMP PEAK 1(2P23.2) MUTATED   11  4 21
  AMP PEAK 1(2P23.2) WILD-TYPE 70  4 75
D1V6, multiclass
    clus
vv   AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE
  M0                         11                           70
  M1                          4                            4
  MX                         21                           75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                              cls
clus                             0   1
  AMP PEAK 1(2P23.2) MUTATED    14  25
  AMP PEAK 1(2P23.2) WILD-TYPE  44 115
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(2P23.2) MUTATED     14   25
  AMP PEAK 1(2P23.2) WILD-TYPE   44  115
        clus
vv       AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE
  FEMALE                         14                           44
  MALE                           25                          115
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 1(2P23.2) MUTATED                                  0     1
  AMP PEAK 1(2P23.2) WILD-TYPE                                2     3
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 1(2P23.2) MUTATED                           7    27
  AMP PEAK 1(2P23.2) WILD-TYPE                        42   102
D1V10, multiclass
                                  clus
vv                                 AMP PEAK 1(2P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 7
  WHITE                                                    27
                                  clus
vv                                 AMP PEAK 1(2P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  42
  WHITE                                                     102
[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"
D1V11, binary
                              cls
clus                             0   1
  AMP PEAK 1(2P23.2) MUTATED     2  32
  AMP PEAK 1(2P23.2) WILD-TYPE   7 121
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(2P23.2) MUTATED      2   32
  AMP PEAK 1(2P23.2) WILD-TYPE    7  121
                        clus
vv                       AMP PEAK 1(2P23.2) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         32
                        clus
vv                       AMP PEAK 1(2P23.2) WILD-TYPE
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          121
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK 2(2Q32.1) MUTATION ANALYSIS
D2V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 2(2Q32.1) MUTATED    37   1
  AMP PEAK 2(2Q32.1) WILD-TYPE 129   6
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                          38                          135 
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                           1                            6 
$`AMP PEAK 2(2Q32.1) MUTATED`
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-AL-3471 TCGA-AL-7173 TCGA-AT-A5NU 
         516            2          118          412         1357           67 
TCGA-B1-7332 TCGA-B3-A6W5 TCGA-B9-4117 TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5878 
         223           85           14           64          102         1938 
TCGA-BQ-5885 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7046 TCGA-DW-5561 TCGA-DZ-6131 
         921          364           84         2948          414         2429 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-7502 TCGA-GL-7966 
          36          208         1575         1194          786          112 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GD 
          91         2072          360          511           62          160 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5EB TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         885          161         1043         2584          174           57 
TCGA-SX-A71V TCGA-SX-A7SQ 
         508          494 

$`AMP PEAK 2(2Q32.1) WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 
          87            4         1778         1636          923          763 
TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
          26          595          659          747          108          510 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
          14         1029          307          930         1049          379 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 
        1536          857          803          627           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH 
        1338          671          585          207            5          167 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5881 TCGA-BQ-5883 
          52         2639          586          270         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
         792          792          771          403          233           29 
TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        3760         2839         1864         1533         1516          799 
TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
         612          232          214          218          116          353 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
         445           92         1240         2460         1856         1670 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
        1040          578          757           97           10            7 
TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LD 
        1479         1059          765          446          279         1967 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-HE-A5NH 
        5925          393          841           32          178          408 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
        1726          167          608          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
           2            4          391          543          438          292 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED 
          11          541          148         3035         2653         2816 
TCGA-PJ-A5Z8 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM 
         391         1079         1199          994          423         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 
         102          925         1247          847          224            2 
TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         186          181          205 

  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                           2                            2 
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                        2948                         5925 
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                         362                          578 
[1] "2.0 - 2948.0 (362.0)" "2.0 - 5925.0 (578.0)"
[1] "hr=" "1.7"
D2V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 2(2Q32.1) MUTATED        24        2        11        7
  AMP PEAK 2(2Q32.1) WILD-TYPE      98        9        31        5
D2V3, multiclass
           clus
vv          AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  STAGE I                           24                           98
  STAGE II                           2                            9
  STAGE III                         11                           31
  STAGE IV                           7                            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                            T1  T2 T3+T4
  AMP PEAK 2(2Q32.1) MUTATED    24   5    16
  AMP PEAK 2(2Q32.1) WILD-TYPE 106  13    34
D2V4, multiclass
       clus
vv      AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  T1                            24                          106
  T2                             5                           13
  T3+T4                         16                           34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2
  AMP PEAK 2(2Q32.1) MUTATED    8  8  2
  AMP PEAK 2(2Q32.1) WILD-TYPE 25 12  2
D2V5, multiclass
    clus
vv   AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  N0                          8                           25
  N1                          8                           12
  N2                          2                            2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1 MX
  AMP PEAK 2(2Q32.1) MUTATED   14  5 22
  AMP PEAK 2(2Q32.1) WILD-TYPE 67  3 74
D2V6, multiclass
    clus
vv   AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  M0                         14                           67
  M1                          5                            3
  MX                         22                           74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                              cls
clus                             0   1
  AMP PEAK 2(2Q32.1) MUTATED    15  30
  AMP PEAK 2(2Q32.1) WILD-TYPE  43 110
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(2Q32.1) MUTATED     15   30
  AMP PEAK 2(2Q32.1) WILD-TYPE   43  110
        clus
vv       AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  FEMALE                         15                           43
  MALE                           30                          110
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 2(2Q32.1) MUTATED                                  0     1
  AMP PEAK 2(2Q32.1) WILD-TYPE                                2     3
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 2(2Q32.1) MUTATED                           7    34
  AMP PEAK 2(2Q32.1) WILD-TYPE                        42    95
D2V10, multiclass
                                  clus
vv                                 AMP PEAK 2(2Q32.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 7
  WHITE                                                    34
                                  clus
vv                                 AMP PEAK 2(2Q32.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  42
  WHITE                                                      95
[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"
D2V11, binary
                              cls
clus                             0   1
  AMP PEAK 2(2Q32.1) MUTATED     2  37
  AMP PEAK 2(2Q32.1) WILD-TYPE   7 116
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(2Q32.1) MUTATED      2   37
  AMP PEAK 2(2Q32.1) WILD-TYPE    7  116
                        clus
vv                       AMP PEAK 2(2Q32.1) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         37
                        clus
vv                       AMP PEAK 2(2Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          116
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK 3(3P12.1) MUTATION ANALYSIS
D3V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 3(3P12.1) MUTATED    48   2
  AMP PEAK 3(3P12.1) WILD-TYPE 118   5
  AMP PEAK 3(3P12.1) MUTATED AMP PEAK 3(3P12.1) WILD-TYPE 
                          50                          123 
  AMP PEAK 3(3P12.1) MUTATED AMP PEAK 3(3P12.1) WILD-TYPE 
                           2                            5 
$`AMP PEAK 3(3P12.1) MUTATED`
TCGA-A4-7287 TCGA-A4-8311 TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
          21          729           23          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 
         516           87         1636          412           67          223 
TCGA-B3-4103 TCGA-B3-A6W5 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         930           85           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A69E TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-7046 
         671          102          167         1454          792         2948 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         214          116          353         1093         1142          744 
TCGA-DW-7963 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-A8LD TCGA-GL-6846 
        1240           10            7         1575         1967         5925 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NL TCGA-KV-A6GD TCGA-KV-A6GE 
          91         2072          360          167          160          885 
TCGA-KV-A74V TCGA-P4-A5E7 TCGA-PJ-A5Z9 TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SQ 
         161         2653          174          508          102          494 
TCGA-SX-A7SS TCGA-Y8-A895 
        1247            2 

$`AMP PEAK 3(3P12.1) WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         554          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8515 TCGA-A4-8517 
          49            2          140          780          709          597 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
           2          118            4         1778          923          763 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
        1357           26          595          659          747          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 
         510           14         1029          307         1049          379 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W7 
        1536          857          803          627           64          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         207            5           52         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 
        1938         1242          792          921          771          403 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 
         233           29          364           84         3760         2839 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
        1864         1533         1516          799          612          232 
TCGA-BQ-7061 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
         218          414         3950          419          114          445 
TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
          92         2429         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6792 
         578          757           97           36          208         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
        1194         1059          765          446          786          279 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-HE-A5NH 
         393          112          841           32          178          408 
TCGA-HE-A5NJ TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        1726          511          608           62          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         146            2            4         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
         438          292           11          541          148         3035 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
        2584         2816          391           57         1079         1199 
TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SU TCGA-Y8-A894 
         994          423         1973          925          847          224 
TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         186          181          205 

  AMP PEAK 3(3P12.1) MUTATED AMP PEAK 3(3P12.1) WILD-TYPE 
                           2                            2 
  AMP PEAK 3(3P12.1) MUTATED AMP PEAK 3(3P12.1) WILD-TYPE 
                        5925                         3950 
  AMP PEAK 3(3P12.1) MUTATED AMP PEAK 3(3P12.1) WILD-TYPE 
                         424                          543 
[1] "2.0 - 5925.0 (424.0)" "2.0 - 3950.0 (543.0)"
[1] "hr=" "1"  
D3V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 3(3P12.1) MUTATED        44        3         8        1
  AMP PEAK 3(3P12.1) WILD-TYPE      78        8        34       11
D3V3, multiclass
           clus
vv          AMP PEAK 3(3P12.1) MUTATED AMP PEAK 3(3P12.1) WILD-TYPE
  STAGE I                           44                           78
  STAGE II                           3                            8
  STAGE III                          8                           34
  STAGE IV                           1                           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                           T1 T2 T3+T4
  AMP PEAK 3(3P12.1) MUTATED   46  5     8
  AMP PEAK 3(3P12.1) WILD-TYPE 84 13    42
D3V4, multiclass
       clus
vv      AMP PEAK 3(3P12.1) MUTATED AMP PEAK 3(3P12.1) WILD-TYPE
  T1                            46                           84
  T2                             5                           13
  T3+T4                          8                           42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2
  AMP PEAK 3(3P12.1) MUTATED    6  4  0
  AMP PEAK 3(3P12.1) WILD-TYPE 27 16  4
D3V5, multiclass
    clus
vv   AMP PEAK 3(3P12.1) MUTATED AMP PEAK 3(3P12.1) WILD-TYPE
  N0                          6                           27
  N1                          4                           16
  N2                          0                            4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1 MX
  AMP PEAK 3(3P12.1) MUTATED   24  0 30
  AMP PEAK 3(3P12.1) WILD-TYPE 57  8 66
D3V6, multiclass
    clus
vv   AMP PEAK 3(3P12.1) MUTATED AMP PEAK 3(3P12.1) WILD-TYPE
  M0                         24                           57
  M1                          0                            8
  MX                         30                           66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                              cls
clus                            0  1
  AMP PEAK 3(3P12.1) MUTATED   15 44
  AMP PEAK 3(3P12.1) WILD-TYPE 43 96
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(3P12.1) MUTATED     15   44
  AMP PEAK 3(3P12.1) WILD-TYPE   43   96
        clus
vv       AMP PEAK 3(3P12.1) MUTATED AMP PEAK 3(3P12.1) WILD-TYPE
  FEMALE                         15                           43
  MALE                           44                           96
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 3(3P12.1) MUTATED                                  1     1
  AMP PEAK 3(3P12.1) WILD-TYPE                                1     3
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 3(3P12.1) MUTATED                          10    41
  AMP PEAK 3(3P12.1) WILD-TYPE                        39    88
D3V10, multiclass
                                  clus
vv                                 AMP PEAK 3(3P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                10
  WHITE                                                    41
                                  clus
vv                                 AMP PEAK 3(3P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  39
  WHITE                                                      88
[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"
D3V11, binary
                              cls
clus                             0   1
  AMP PEAK 3(3P12.1) MUTATED     2  47
  AMP PEAK 3(3P12.1) WILD-TYPE   7 106
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(3P12.1) MUTATED      2   47
  AMP PEAK 3(3P12.1) WILD-TYPE    7  106
                        clus
vv                       AMP PEAK 3(3P12.1) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         47
                        clus
vv                       AMP PEAK 3(3P12.1) WILD-TYPE
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          106
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK 4(3Q26.31) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 4(3Q26.31) MUTATED    62   1
  AMP PEAK 4(3Q26.31) WILD-TYPE 104   6
  AMP PEAK 4(3Q26.31) MUTATED AMP PEAK 4(3Q26.31) WILD-TYPE 
                           63                           110 
  AMP PEAK 4(3Q26.31) MUTATED AMP PEAK 4(3Q26.31) WILD-TYPE 
                            1                             6 
$`AMP PEAK 4(3Q26.31) MUTATED`
TCGA-A4-7287 TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8518 
          21            2          729          709           23          600 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-AL-3468 TCGA-AL-3471 
         436          379          516            2         1636          412 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B3-4103 TCGA-B3-A6W5 TCGA-B9-4114 
          67          223          659          930           85          857 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
          14           35          460         1338          671           64 
TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-7046 TCGA-BQ-7060 
         167         1454          792          233         2948          214 
TCGA-BQ-7062 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6131 
         116         1093         1142          744         1240         2429 
TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6790 
        2460         1670         1040           10            7         1575 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NL 
        1967         5925           91         2072          360          167 
TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5E6 
          62          160          885          161         1043         3035 
TCGA-P4-A5E7 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SQ 
        2653          174           57          508          102          494 
TCGA-SX-A7SS TCGA-Y8-A895 TCGA-Y8-A8RZ 
        1247            2          205 

$`AMP PEAK 4(3Q26.31) WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         554          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8517 TCGA-A4-A5Y0 TCGA-A4-A5Y1 
          49          140          780          597          118           87 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
           4         1778          923          763         1357           26 
TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         595          747          108          510           14         1029 
TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 
         307         1049          379         1536          803          627 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 
         585          207            5          102           52         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         586          270         1938         1242          792          921 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
         771          403           29          364           84         3760 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2839         1864         1533         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7839 
         232          218          353          414         3950          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-EV-5902 TCGA-EV-5903 
         114          445           92         1856          578          757 
TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
          97           36          208         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-7773 TCGA-GL-7966 
         765          446          786          279          393          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-IA-A40U 
         841           32          178          408         1726          511 
TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
         608          677          649          146            2            4 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-SX-A71R TCGA-SX-A71S 
         148         2584         2816          391         1079         1199 
TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SU TCGA-Y8-A894 
         994          423         1973          925          847          224 
TCGA-Y8-A896 TCGA-Y8-A898 
         186          181 

  AMP PEAK 4(3Q26.31) MUTATED AMP PEAK 4(3Q26.31) WILD-TYPE 
                            2                             2 
  AMP PEAK 4(3Q26.31) MUTATED AMP PEAK 4(3Q26.31) WILD-TYPE 
                         5925                          3950 
  AMP PEAK 4(3Q26.31) MUTATED AMP PEAK 4(3Q26.31) WILD-TYPE 
                        494.0                         510.5 
[1] "2.0 - 5925.0 (494.0)" "2.0 - 3950.0 (510.5)"
[1] "hr=" "4.2"
D4V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 4(3Q26.31) MUTATED        50        4        13        2
  AMP PEAK 4(3Q26.31) WILD-TYPE      72        7        29       10
D4V3, multiclass
           clus
vv          AMP PEAK 4(3Q26.31) MUTATED AMP PEAK 4(3Q26.31) WILD-TYPE
  STAGE I                            50                            72
  STAGE II                            4                             7
  STAGE III                          13                            29
  STAGE IV                            2                            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                            T1 T2 T3+T4
  AMP PEAK 4(3Q26.31) MUTATED   52  7    14
  AMP PEAK 4(3Q26.31) WILD-TYPE 78 11    36
D4V4, multiclass
       clus
vv      AMP PEAK 4(3Q26.31) MUTATED AMP PEAK 4(3Q26.31) WILD-TYPE
  T1                             52                            78
  T2                              7                            11
  T3+T4                          14                            36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  AMP PEAK 4(3Q26.31) MUTATED    9  5  1
  AMP PEAK 4(3Q26.31) WILD-TYPE 24 15  3
D4V5, multiclass
    clus
vv   AMP PEAK 4(3Q26.31) MUTATED AMP PEAK 4(3Q26.31) WILD-TYPE
  N0                           9                            24
  N1                           5                            15
  N2                           1                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  AMP PEAK 4(3Q26.31) MUTATED   26  0 41
  AMP PEAK 4(3Q26.31) WILD-TYPE 55  8 55
D4V6, multiclass
    clus
vv   AMP PEAK 4(3Q26.31) MUTATED AMP PEAK 4(3Q26.31) WILD-TYPE
  M0                          26                            55
  M1                           0                             8
  MX                          41                            55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                               cls
clus                             0  1
  AMP PEAK 4(3Q26.31) MUTATED   19 54
  AMP PEAK 4(3Q26.31) WILD-TYPE 39 86
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(3Q26.31) MUTATED     19   54
  AMP PEAK 4(3Q26.31) WILD-TYPE   39   86
        clus
vv       AMP PEAK 4(3Q26.31) MUTATED AMP PEAK 4(3Q26.31) WILD-TYPE
  FEMALE                          19                            39
  MALE                            54                            86
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 4(3Q26.31) MUTATED                                  2     1
  AMP PEAK 4(3Q26.31) WILD-TYPE                                0     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 4(3Q26.31) MUTATED                          16    46
  AMP PEAK 4(3Q26.31) WILD-TYPE                        33    83
D4V10, multiclass
                                  clus
vv                                 AMP PEAK 4(3Q26.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                     46
                                  clus
vv                                 AMP PEAK 4(3Q26.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   33
  WHITE                                                       83
[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"
D4V11, binary
                               cls
clus                             0  1
  AMP PEAK 4(3Q26.31) MUTATED    2 57
  AMP PEAK 4(3Q26.31) WILD-TYPE  7 96
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(3Q26.31) MUTATED      2   57
  AMP PEAK 4(3Q26.31) WILD-TYPE    7   96
                        clus
vv                       AMP PEAK 4(3Q26.31) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          57
                        clus
vv                       AMP PEAK 4(3Q26.31) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            96
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK 5(7Q22.1) MUTATION ANALYSIS
D5V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 5(7Q22.1) MUTATED   107   3
  AMP PEAK 5(7Q22.1) WILD-TYPE  59   4
  AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE 
                         110                           63 
  AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE 
                           3                            4 
$`AMP PEAK 5(7Q22.1) MUTATED`
TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 
         493          582           27           49            2          780 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A4ZT 
         729          709           23          597          436          516 
TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 
           2            4         1636          412          923         1357 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 
          26           67          659          747          108           14 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
        1029          930          379           85         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5887 
         671          585          167         1454          792          771 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7051 
          29          364           84         3760         2948         1533 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7840 TCGA-DW-7841 
        3950         1093         1142          744          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 
          92         1240         2460         1856         1040          757 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 
          10            7           36          208         1575         1194 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R 
         786          279         5925          112          841          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40Y TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE 
          62          649          146            2          160          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 
         161         1043          391          292          148         2653 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         174           57         1079         1199          994          508 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A895 
        1973          102          494         1247          847            2 
TCGA-Y8-A896 TCGA-Y8-A898 
         186          181 

$`AMP PEAK 5(7Q22.1) WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8518 
         554           21            3            7          140          600 
TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 
         379          118           87         1778          763          595 
TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-A44B TCGA-B9-A5W8 
         223          510          307         1049           64          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
           5          102           52         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 
        1938         1242          921          792          403          233 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-DW-7839 
        2839         1864         1516          799          612          419 
TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-G7-6792 TCGA-G7-6796 
        2429         1670          578           97         1479         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-A4EM TCGA-IA-A40U 
         765          446         1967          393           32          511 
TCGA-IA-A40X TCGA-IZ-8195 TCGA-J7-8537 TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A854 
         608          677            4          543          438           11 
TCGA-MH-A856 TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-SX-A7SL 
         541         3035         2584         2816          391          423 
TCGA-SX-A7SO TCGA-Y8-A894 TCGA-Y8-A8RZ 
         925          224          205 

  AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE 
                           2                            3 
  AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE 
                        5925                         3035 
  AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE 
                       476.5                        541.0 
[1] "2.0 - 5925.0 (476.5)" "3.0 - 3035.0 (541.0)"
[1] "hr=" "1.9"
D5V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 5(7Q22.1) MUTATED        86        4        15        8
  AMP PEAK 5(7Q22.1) WILD-TYPE      36        7        27        4
D5V3, multiclass
           clus
vv          AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE
  STAGE I                           86                           36
  STAGE II                           4                            7
  STAGE III                         15                           27
  STAGE IV                           8                            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                           T1 T2 T3+T4
  AMP PEAK 5(7Q22.1) MUTATED   89 11    22
  AMP PEAK 5(7Q22.1) WILD-TYPE 41  7    28
D5V4, multiclass
       clus
vv      AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE
  T1                            89                           41
  T2                            11                            7
  T3+T4                         22                           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"
                              vv
clus                           N0 N1 N2
  AMP PEAK 5(7Q22.1) MUTATED   17  7  2
  AMP PEAK 5(7Q22.1) WILD-TYPE 16 13  2
D5V5, multiclass
    clus
vv   AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE
  N0                         17                           16
  N1                          7                           13
  N2                          2                            2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1 MX
  AMP PEAK 5(7Q22.1) MUTATED   46  5 61
  AMP PEAK 5(7Q22.1) WILD-TYPE 35  3 35
D5V6, multiclass
    clus
vv   AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE
  M0                         46                           35
  M1                          5                            3
  MX                         61                           35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                              cls
clus                            0  1
  AMP PEAK 5(7Q22.1) MUTATED   31 91
  AMP PEAK 5(7Q22.1) WILD-TYPE 27 49
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(7Q22.1) MUTATED     31   91
  AMP PEAK 5(7Q22.1) WILD-TYPE   27   49
        clus
vv       AMP PEAK 5(7Q22.1) MUTATED AMP PEAK 5(7Q22.1) WILD-TYPE
  FEMALE                         31                           27
  MALE                           91                           49
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 5(7Q22.1) MUTATED                                  2     3
  AMP PEAK 5(7Q22.1) WILD-TYPE                                0     1
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 5(7Q22.1) MUTATED                          30    76
  AMP PEAK 5(7Q22.1) WILD-TYPE                        19    53
D5V10, multiclass
                                  clus
vv                                 AMP PEAK 5(7Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          2
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                30
  WHITE                                                    76
                                  clus
vv                                 AMP PEAK 5(7Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  19
  WHITE                                                      53
[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"
D5V11, binary
                              cls
clus                            0  1
  AMP PEAK 5(7Q22.1) MUTATED    4 99
  AMP PEAK 5(7Q22.1) WILD-TYPE  5 54
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(7Q22.1) MUTATED      4   99
  AMP PEAK 5(7Q22.1) WILD-TYPE    5   54
                        clus
vv                       AMP PEAK 5(7Q22.1) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                         99
                        clus
vv                       AMP PEAK 5(7Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           54
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK 6(17Q25.2) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 6(17Q25.2) MUTATED   123   5
  AMP PEAK 6(17Q25.2) WILD-TYPE  43   2
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                          128                            45 
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                            5                             2 
$`AMP PEAK 6(17Q25.2) MUTATED`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
         554          493          582           27            7           49 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
         140          780          729          709           23          597 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         600          436          516            2          118           87 
TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-A5DJ TCGA-AT-A5NU 
           4         1636          412          923           26           67 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3925 
         223          659          747          108          510         1029 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379           85         1536          857 
TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         803           14           35          460         1338          671 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5875 TCGA-BQ-5877 
          64          585            5          167         2639          270 
TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
        1454          792          771          403          233           29 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7060 TCGA-BQ-7062 
         364         2948         1533         1516          214          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         353          414         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
         419          114          445           92         1240         2429 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF 
        2460         1856         1040          757           10            7 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 
          36          208         1575         1194         1059          786 
TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R 
         279         1967         5925          112           32          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         511           62          677          649          146            2 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
           4          160          885          161         1043          391 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5EB 
         543          438          292          148         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2816          174           57         1079         1199          994 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU 
         508          423          102          494         1247          847 
TCGA-Y8-A895 TCGA-Y8-A898 
           2          181 

$`AMP PEAK 6(17Q25.2) WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7997 TCGA-A4-A48D TCGA-AL-3467 TCGA-AL-3473 
          21            3            2          379         1778          763 
TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A656 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A5W8 
        1357          595           14          307          627          207 
TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5884 
         102           52          586         1938         1242          792 
TCGA-BQ-5885 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7055 
         921           84         3760         2839         1864          799 
TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ 
         612          232          218         1670          578           97 
TCGA-G7-6792 TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-7773 TCGA-GL-8500 TCGA-IA-A40X 
        1479          765          446          393          841          608 
TCGA-MH-A854 TCGA-MH-A856 TCGA-P4-A5E6 TCGA-PJ-A5Z8 TCGA-SX-A7SM TCGA-SX-A7SO 
          11          541         3035          391         1973          925 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8RZ 
         224          186          205 

  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                            2                             2 
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                         5925                          3760 
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                        476.5                         586.0 
[1] "2.0 - 5925.0 (476.5)" "2.0 - 3760.0 (586.0)"
[1] "hr=" "1"  
D6V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 6(17Q25.2) MUTATED        94        8        26        8
  AMP PEAK 6(17Q25.2) WILD-TYPE      28        3        16        4
D6V3, multiclass
           clus
vv          AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  STAGE I                            94                            28
  STAGE II                            8                             3
  STAGE III                          26                            16
  STAGE IV                            8                             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                            T1 T2 T3+T4
  AMP PEAK 6(17Q25.2) MUTATED   98 14    33
  AMP PEAK 6(17Q25.2) WILD-TYPE 32  4    17
D6V4, multiclass
       clus
vv      AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  T1                             98                            32
  T2                             14                             4
  T3+T4                          33                            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"
                               vv
clus                            N0 N1 N2
  AMP PEAK 6(17Q25.2) MUTATED   23 12  3
  AMP PEAK 6(17Q25.2) WILD-TYPE 10  8  1
D6V5, multiclass
    clus
vv   AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  N0                          23                            10
  N1                          12                             8
  N2                           3                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  AMP PEAK 6(17Q25.2) MUTATED   50  5 79
  AMP PEAK 6(17Q25.2) WILD-TYPE 31  3 17
D6V6, multiclass
    clus
vv   AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  M0                          50                            31
  M1                           5                             3
  MX                          79                            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"
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK 6(17Q25.2) MUTATED    37 108
  AMP PEAK 6(17Q25.2) WILD-TYPE  21  32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(17Q25.2) MUTATED     37  108
  AMP PEAK 6(17Q25.2) WILD-TYPE   21   32
        clus
vv       AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  FEMALE                          37                            21
  MALE                           108                            32
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 6(17Q25.2) MUTATED                                  2     4
  AMP PEAK 6(17Q25.2) WILD-TYPE                                0     0
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 6(17Q25.2) MUTATED                          33    96
  AMP PEAK 6(17Q25.2) WILD-TYPE                        16    33
D6V10, multiclass
                                  clus
vv                                 AMP PEAK 6(17Q25.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 33
  WHITE                                                     96
                                  clus
vv                                 AMP PEAK 6(17Q25.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                       33
[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"
D6V11, binary
                               cls
clus                              0   1
  AMP PEAK 6(17Q25.2) MUTATED     6 116
  AMP PEAK 6(17Q25.2) WILD-TYPE   3  37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(17Q25.2) MUTATED      6  116
  AMP PEAK 6(17Q25.2) WILD-TYPE    3   37
                        clus
vv                       AMP PEAK 6(17Q25.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         116
                        clus
vv                       AMP PEAK 6(17Q25.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            37
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK 7(19P13.2) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 7(19P13.2) MUTATED    19   1
  AMP PEAK 7(19P13.2) WILD-TYPE 147   6
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                           20                           153 
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                            1                             6 
$`AMP PEAK 7(19P13.2) MUTATED`
TCGA-A4-7732 TCGA-A4-A5XZ TCGA-AL-3472 TCGA-B9-4113 TCGA-B9-4116 TCGA-B9-4617 
         582            2          923         1536          627           35 
TCGA-BQ-5885 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-DW-5561 TCGA-DW-7840 TCGA-EV-5901 
         921           29          364          414          114         1040 
TCGA-F9-A7Q0 TCGA-G7-6795 TCGA-G7-A4TM TCGA-GL-7966 TCGA-HE-A5NJ TCGA-IZ-8196 
          10         1194          279          112         1726          649 
TCGA-P4-A5E7 TCGA-SX-A7SU 
        2653          847 

$`AMP PEAK 7(19P13.2) WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7734 TCGA-A4-7915 
         554           21          493            3           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
         118           87            4         1778         1636          412 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
         763         1357           26           67          595          223 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         659          747          108          510           14         1029 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4114 
         307          930         1049          379           85          857 
TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
         803           14          460         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
         585          207            5          102          167           52 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
        2639          586          270         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5894 
         792          792          771          403          233           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         799          612          232          214          218          116 
TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         353         3950         1093         1142          744          419 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
         445           92         1240         2429         2460         1856 
TCGA-DZ-6135 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY 
        1670          578          757           97            7           36 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
         208         1575         1479         1059          765          446 
TCGA-G7-7502 TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
         786         1967         5925          393          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NL 
         178           91         2072          408          360          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         511          608           62          677          146            2 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
           4          160          885          161         1043          391 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
         543          438          292           11          541          148 
TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        3035         2584         2816          391          174           57 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
        1079         1199          994          508          423         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-Y8-A894 TCGA-Y8-A895 
         102          925          494         1247          224            2 
TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         186          181          205 

  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                            2                             2 
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                         2653                          5925 
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                        604.5                         494.0 
[1] "2.0 - 2653.0 (604.5)" "2.0 - 5925.0 (494.0)"
[1] "hr=" "1.4"
D7V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 7(19P13.2) MUTATED        13        1         3        0
  AMP PEAK 7(19P13.2) WILD-TYPE     109       10        39       12
D7V3, multiclass
           clus
vv          AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  STAGE I                            13                           109
  STAGE II                            1                            10
  STAGE III                           3                            39
  STAGE IV                            0                            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                             T1  T2 T3+T4
  AMP PEAK 7(19P13.2) MUTATED    14   5     3
  AMP PEAK 7(19P13.2) WILD-TYPE 116  13    47
D7V4, multiclass
       clus
vv      AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  T1                             14                           116
  T2                              5                            13
  T3+T4                           3                            47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  AMP PEAK 7(19P13.2) MUTATED    5  1  0
  AMP PEAK 7(19P13.2) WILD-TYPE 28 19  4
D7V5, multiclass
    clus
vv   AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  N0                           5                            28
  N1                           1                            19
  N2                           0                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  AMP PEAK 7(19P13.2) MUTATED   11  0  9
  AMP PEAK 7(19P13.2) WILD-TYPE 70  8 87
D7V6, multiclass
    clus
vv   AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  M0                          11                            70
  M1                           0                             8
  MX                           9                            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK 7(19P13.2) MUTATED     8  14
  AMP PEAK 7(19P13.2) WILD-TYPE  50 126
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 7(19P13.2) MUTATED      8   14
  AMP PEAK 7(19P13.2) WILD-TYPE   50  126
        clus
vv       AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  FEMALE                           8                            50
  MALE                            14                           126
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
[1] "Remove cluster labels:"      "AMP PEAK 7(19P13.2) MUTATED"
clus
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                            2                            22 
                   TCGA-A4-A48D                    TCGA-B1-A654 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-B9-A44B                    TCGA-B9-A69E 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-G7-A8LD                    TCGA-GL-7773 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-GL-A59T                    TCGA-HE-A5NI 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-IA-A40U                    TCGA-MH-A854 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-MH-A856                    TCGA-P4-A5EB 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-PJ-A5Z9                    TCGA-Q2-A5QZ 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-SX-A71S                    TCGA-SX-A71U 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-SX-A7SL                    TCGA-SX-A7SM 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-SX-A7SS                    TCGA-Y8-A894 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-Y8-A896                    TCGA-Y8-A8RZ 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 7(19P13.2) MUTATED                                  0     1
  AMP PEAK 7(19P13.2) WILD-TYPE                                2     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 7(19P13.2) MUTATED                           8    10
  AMP PEAK 7(19P13.2) WILD-TYPE                        41   119
D7V10, multiclass
                                  clus
vv                                 AMP PEAK 7(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     10
                                  clus
vv                                 AMP PEAK 7(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   41
  WHITE                                                      119
[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"
D7V11, binary
                               cls
clus                              0   1
  AMP PEAK 7(19P13.2) MUTATED     1  18
  AMP PEAK 7(19P13.2) WILD-TYPE   8 135
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 7(19P13.2) MUTATED      1   18
  AMP PEAK 7(19P13.2) WILD-TYPE    8  135
                        clus
vv                       AMP PEAK 7(19P13.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          18
                        clus
vv                       AMP PEAK 7(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           135
[1] 2 2
[1] FALSE

Clustering(8) Variable = DEL PEAK  1(1P36.32) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.32) MUTATED    29   5
  DEL PEAK  1(1P36.32) WILD-TYPE 137   2
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            34                            139 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                             5                              2 
$`DEL PEAK  1(1P36.32) MUTATED`
TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-8098 TCGA-A4-A5XZ TCGA-A4-A5Y1 TCGA-AL-A5DJ 
         554            3          140            2           87           26 
TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A69E 
         223          307          627           64          207          102 
TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5894 
        2639          270          921          403          233           84 
TCGA-BQ-7044 TCGA-BQ-7055 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6797 
        3760          799           97           10          208          765 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LD TCGA-GL-7966 TCGA-GL-8500 TCGA-IA-A40Y 
         446          786         1967          112          841           62 
TCGA-J7-8537 TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-Y8-A8RZ 
           4          391           57          205 

$`DEL PEAK  1(1P36.32) WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
          21          493          582           27            7           49 
TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
           2          780          729          709           23          597 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5Y0 TCGA-A4-A6HP 
         600          436          379          516          118            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
          67          595          659          747          108          510 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
          14         1029          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
        1536          857          803           14           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI 
        1338          671          585            5          167           52 
TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 
         586         1938         1454         1242          792          792 
TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
         771           29          364         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1533         1516          612          232          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
         116          353          414         3950         1093         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          445           92         1240 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        2429         2460         1856         1670         1040          578 
TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
         757            7           36         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-A4EM TCGA-GL-A59R 
        1059          279         5925          393           32          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         511          608          677          649          146            2 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         160          885          161         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
         438          292           11          541          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
        2653         2584         2816          174         1079         1199 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
         994          508          423         1973          102          925 
TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
         494         1247          847          224            2          186 
TCGA-Y8-A898 
         181 

  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                             2                              2 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                          3760                           5925 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                         215.5                          582.0 
[1] "2.0 - 3760.0 (215.5)" "2.0 - 5925.0 (582.0)"
[1] "hr=" "14" 
D8V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  1(1P36.32) MUTATED        10        3        19        5
  DEL PEAK  1(1P36.32) WILD-TYPE     112        8        23        7
D8V3, multiclass
           clus
vv          DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  STAGE I                             10                            112
  STAGE II                             3                              8
  STAGE III                           19                             23
  STAGE IV                             5                              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                              T1  T2 T3+T4
  DEL PEAK  1(1P36.32) MUTATED    12   5    22
  DEL PEAK  1(1P36.32) WILD-TYPE 118  13    28
D8V4, multiclass
       clus
vv      DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  T1                              12                            118
  T2                               5                             13
  T3+T4                           22                             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"
                                vv
clus                             N0 N1 N2
  DEL PEAK  1(1P36.32) MUTATED    7 11  1
  DEL PEAK  1(1P36.32) WILD-TYPE 26  9  3
D8V5, multiclass
    clus
vv   DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  N0                            7                             26
  N1                           11                              9
  N2                            1                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK  1(1P36.32) MUTATED   14  4 17
  DEL PEAK  1(1P36.32) WILD-TYPE 67  4 79
D8V6, multiclass
    clus
vv   DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  M0                           14                             67
  M1                            4                              4
  MX                           17                             79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED    18  21
  DEL PEAK  1(1P36.32) WILD-TYPE  40 119
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED     18   21
  DEL PEAK  1(1P36.32) WILD-TYPE   40  119
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  FEMALE                           18                             40
  MALE                             21                            119
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P36.32) MUTATED                                  0     2
  DEL PEAK  1(1P36.32) WILD-TYPE                                2     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.32) MUTATED                          10    25
  DEL PEAK  1(1P36.32) WILD-TYPE                        39   104
D8V10, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      25
                                  clus
vv                                 DEL PEAK  1(1P36.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    39
  WHITE                                                       104
[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"
D8V11, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED     1  30
  DEL PEAK  1(1P36.32) WILD-TYPE   8 123
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED      1   30
  DEL PEAK  1(1P36.32) WILD-TYPE    8  123
                        clus
vv                       DEL PEAK  1(1P36.32) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           30
                        clus
vv                       DEL PEAK  1(1P36.32) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            123
[1] 2 2
[1] FALSE

Clustering(9) Variable = DEL PEAK  2(2Q37.3) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(2Q37.3) MUTATED     7   0
  DEL PEAK  2(2Q37.3) WILD-TYPE 159   7
  DEL PEAK  2(2Q37.3) MUTATED DEL PEAK  2(2Q37.3) WILD-TYPE 
                            7                           166 
  DEL PEAK  2(2Q37.3) MUTATED DEL PEAK  2(2Q37.3) WILD-TYPE 
                            0                             7 
$`DEL PEAK  2(2Q37.3) MUTATED`
TCGA-A4-A5Y0 TCGA-B3-4104 TCGA-B9-4117 TCGA-B9-A69E TCGA-BQ-5878 TCGA-Q2-A5QZ 
         118         1049           14          102         1938           57 
TCGA-Y8-A8RZ 
         205 

$`DEL PEAK  2(2Q37.3) WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
         516            2           87            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
         412          923          763         1357           26           67 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
         595          223          659          747          108          510 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 
          14         1029          307          930          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 
        1536          857          803          627           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
        1338          671           64          585          207            5 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5881 
         167           52         2639          586          270         1454 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
        1242          792          921          792          771          403 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 
         233           29          364           84         3760         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2839         1864         1533         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
         445           92         1240         2429         2460         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
        1670         1040          578          757           97           10 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
           7           36          208         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD 
        1059          765          446          786          279         1967 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         511          608           62          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
           2            4          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         148         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
         174         1079         1199          994          508          423 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU 
        1973          102          925          494         1247          847 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 
         224            2          186          181 

  DEL PEAK  2(2Q37.3) MUTATED DEL PEAK  2(2Q37.3) WILD-TYPE 
                           14                             2 
  DEL PEAK  2(2Q37.3) MUTATED DEL PEAK  2(2Q37.3) WILD-TYPE 
                         1938                          5925 
  DEL PEAK  2(2Q37.3) MUTATED DEL PEAK  2(2Q37.3) WILD-TYPE 
                        118.0                         510.5 
[1] "14.0 - 1938.0 (118.0)" "2.0 - 5925.0 (510.5)" 
[1] "hr="     "2.5e+07"
D9V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  2(2Q37.3) MUTATED         2        1         5        0
  DEL PEAK  2(2Q37.3) WILD-TYPE     120       10        37       12
D9V3, multiclass
           clus
vv          DEL PEAK  2(2Q37.3) MUTATED DEL PEAK  2(2Q37.3) WILD-TYPE
  STAGE I                             2                           120
  STAGE II                            1                            10
  STAGE III                           5                            37
  STAGE IV                            0                            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                             T1  T2 T3+T4
  DEL PEAK  2(2Q37.3) MUTATED     2   2     5
  DEL PEAK  2(2Q37.3) WILD-TYPE 128  16    45
D9V4, multiclass
       clus
vv      DEL PEAK  2(2Q37.3) MUTATED DEL PEAK  2(2Q37.3) WILD-TYPE
  T1                              2                           128
  T2                              2                            16
  T3+T4                           5                            45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  2(2Q37.3) MUTATED    2  1  0
  DEL PEAK  2(2Q37.3) WILD-TYPE 31 19  4
D9V5, multiclass
    clus
vv   DEL PEAK  2(2Q37.3) MUTATED DEL PEAK  2(2Q37.3) WILD-TYPE
  N0                           2                            31
  N1                           1                            19
  N2                           0                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  DEL PEAK  2(2Q37.3) MUTATED    4  0  3
  DEL PEAK  2(2Q37.3) WILD-TYPE 77  8 93
D9V6, multiclass
    clus
vv   DEL PEAK  2(2Q37.3) MUTATED DEL PEAK  2(2Q37.3) WILD-TYPE
  M0                           4                            77
  M1                           0                             8
  MX                           3                            93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(2Q37.3) MUTATED     5   4
  DEL PEAK  2(2Q37.3) WILD-TYPE  53 136
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2Q37.3) MUTATED      5    4
  DEL PEAK  2(2Q37.3) WILD-TYPE   53  136
        clus
vv       DEL PEAK  2(2Q37.3) MUTATED DEL PEAK  2(2Q37.3) WILD-TYPE
  FEMALE                           5                            53
  MALE                             4                           136
[1] 2 2
[1] FALSE
D9V8, continuous
[1] "Remove cluster labels:"      "DEL PEAK  2(2Q37.3) MUTATED"
clus
  DEL PEAK  2(2Q37.3) MUTATED DEL PEAK  2(2Q37.3) WILD-TYPE 
                            1                            51 
                   TCGA-A4-7286                    TCGA-A4-7828 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-A4-8310                    TCGA-A4-8311 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-A4-8312                    TCGA-A4-8518 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-A4-8630                    TCGA-A4-A4ZT 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-A4-A57E                    TCGA-A4-A5DU 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-A4-A5XZ                    TCGA-A4-A6HP 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-AL-3466                    TCGA-DW-5560 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-DW-5561                    TCGA-DW-7834 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-DW-7836                    TCGA-DW-7837 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-DW-7838                    TCGA-DW-7839 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-DW-7840                    TCGA-DW-7841 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-DW-7842                    TCGA-DW-7963 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-EV-5901                    TCGA-EV-5902 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-EV-5903                    TCGA-G7-6790 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-G7-6793                    TCGA-G7-6796 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-G7-6797                    TCGA-G7-7501 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-G7-7502                    TCGA-G7-A4TM 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-G7-A8LD                    TCGA-IA-A40U 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-IA-A40X                    TCGA-IA-A40Y 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-J7-8537                    TCGA-SX-A71R 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A71S                    TCGA-SX-A71U 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A71V                    TCGA-SX-A7SL 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A7SM                    TCGA-SX-A7SN 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A7SO                    TCGA-SX-A7SP 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A7SQ                    TCGA-SX-A7SS 
"DEL PEAK  2(2Q37.3) WILD-TYPE" "DEL PEAK  2(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A7SU 
"DEL PEAK  2(2Q37.3) WILD-TYPE" 
D9V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(2Q37.3) MUTATED                                  0     0
  DEL PEAK  2(2Q37.3) WILD-TYPE                                2     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(2Q37.3) MUTATED                           2     6
  DEL PEAK  2(2Q37.3) WILD-TYPE                        47   123
D9V10, multiclass
                                  clus
vv                                 DEL PEAK  2(2Q37.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                      6
                                  clus
vv                                 DEL PEAK  2(2Q37.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   47
  WHITE                                                      123
[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"
D9V11, binary
                               cls
clus                              0   1
  DEL PEAK  2(2Q37.3) MUTATED     0   7
  DEL PEAK  2(2Q37.3) WILD-TYPE   9 146
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2Q37.3) MUTATED      0    7
  DEL PEAK  2(2Q37.3) WILD-TYPE    9  146
                        clus
vv                       DEL PEAK  2(2Q37.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           7
                        clus
vv                       DEL PEAK  2(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           146
[1] 2 2
[1] FALSE

Clustering(10) Variable = DEL PEAK  3(3P22.1) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(3P22.1) MUTATED    11   4
  DEL PEAK  3(3P22.1) WILD-TYPE 155   3
  DEL PEAK  3(3P22.1) MUTATED DEL PEAK  3(3P22.1) WILD-TYPE 
                           15                           158 
  DEL PEAK  3(3P22.1) MUTATED DEL PEAK  3(3P22.1) WILD-TYPE 
                            4                             3 
$`DEL PEAK  3(3P22.1) MUTATED`
TCGA-A4-A5Y1 TCGA-AL-3473 TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5892 
          87          763           64          102          270          364 
TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7966 TCGA-IA-A40Y 
        2429          208          446         1967          112           62 
TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-Y8-A8RZ 
           4           57          205 

$`DEL PEAK  3(3P22.1) WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
         516            2          118            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         412          923         1357           26           67          595 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         223          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          857          803          627           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
         460         1338          671          585          207            5 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5881 
         167           52         2639          586         1938         1454 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
        1242          792          921          792          771          403 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 
         233           29           84         3760         2948         2839 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
        1864         1533         1516          799          612          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        1093         1142          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
          92         1240         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
         578          757           97           10            7           36 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 
        1575         1479         1194         1059          765          786 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
         279         5925          393          841           32          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         511          608          677          649          146            2 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         160          885          161         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
         438          292           11          541          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R 
        2653         2584         2816          391          174         1079 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1199          994          508          423         1973          102 
TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 
         925          494         1247          847          224            2 
TCGA-Y8-A896 TCGA-Y8-A898 
         186          181 

  DEL PEAK  3(3P22.1) MUTATED DEL PEAK  3(3P22.1) WILD-TYPE 
                            4                             2 
  DEL PEAK  3(3P22.1) MUTATED DEL PEAK  3(3P22.1) WILD-TYPE 
                         2429                          5925 
  DEL PEAK  3(3P22.1) MUTATED DEL PEAK  3(3P22.1) WILD-TYPE 
                          205                           542 
[1] "4.0 - 2429.0 (205.0)" "2.0 - 5925.0 (542.0)"
[1] "hr=" "16" 
D10V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  3(3P22.1) MUTATED         2        1        11        3
  DEL PEAK  3(3P22.1) WILD-TYPE     120       10        31        9
D10V3, multiclass
           clus
vv          DEL PEAK  3(3P22.1) MUTATED DEL PEAK  3(3P22.1) WILD-TYPE
  STAGE I                             2                           120
  STAGE II                            1                            10
  STAGE III                          11                            31
  STAGE IV                            3                             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                             T1  T2 T3+T4
  DEL PEAK  3(3P22.1) MUTATED     3   2    12
  DEL PEAK  3(3P22.1) WILD-TYPE 127  16    38
D10V4, multiclass
       clus
vv      DEL PEAK  3(3P22.1) MUTATED DEL PEAK  3(3P22.1) WILD-TYPE
  T1                              3                           127
  T2                              2                            16
  T3+T4                          12                            38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  3(3P22.1) MUTATED    6  7  1
  DEL PEAK  3(3P22.1) WILD-TYPE 27 13  3
D10V5, multiclass
    clus
vv   DEL PEAK  3(3P22.1) MUTATED DEL PEAK  3(3P22.1) WILD-TYPE
  N0                           6                            27
  N1                           7                            13
  N2                           1                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  DEL PEAK  3(3P22.1) MUTATED    4  2  9
  DEL PEAK  3(3P22.1) WILD-TYPE 77  6 87
D10V6, multiclass
    clus
vv   DEL PEAK  3(3P22.1) MUTATED DEL PEAK  3(3P22.1) WILD-TYPE
  M0                           4                            77
  M1                           2                             6
  MX                           9                            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(3P22.1) MUTATED     6  11
  DEL PEAK  3(3P22.1) WILD-TYPE  52 129
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(3P22.1) MUTATED      6   11
  DEL PEAK  3(3P22.1) WILD-TYPE   52  129
        clus
vv       DEL PEAK  3(3P22.1) MUTATED DEL PEAK  3(3P22.1) WILD-TYPE
  FEMALE                           6                            52
  MALE                            11                           129
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(3P22.1) MUTATED                                  0     1
  DEL PEAK  3(3P22.1) WILD-TYPE                                2     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(3P22.1) MUTATED                           4    11
  DEL PEAK  3(3P22.1) WILD-TYPE                        45   118
D10V10, multiclass
                                  clus
vv                                 DEL PEAK  3(3P22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     11
                                  clus
vv                                 DEL PEAK  3(3P22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   45
  WHITE                                                      118
[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"
D10V11, binary
                               cls
clus                              0   1
  DEL PEAK  3(3P22.1) MUTATED     0  14
  DEL PEAK  3(3P22.1) WILD-TYPE   9 139
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(3P22.1) MUTATED      0   14
  DEL PEAK  3(3P22.1) WILD-TYPE    9  139
                        clus
vv                       DEL PEAK  3(3P22.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          14
                        clus
vv                       DEL PEAK  3(3P22.1) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           139
[1] 2 2
[1] FALSE

Clustering(11) Variable = DEL PEAK  4(4Q34.3) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(4Q34.3) MUTATED    17   2
  DEL PEAK  4(4Q34.3) WILD-TYPE 149   5
  DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE 
                           19                           154 
  DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE 
                            2                             5 
$`DEL PEAK  4(4Q34.3) MUTATED`
TCGA-A4-7287 TCGA-A4-8098 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B3-3926 
          21          140           87           26          223          307 
TCGA-B3-4104 TCGA-BQ-5876 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-DZ-6131 TCGA-F9-A4JJ 
        1049          586          233           84         2429           97 
TCGA-F9-A7Q0 TCGA-G7-7501 TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ 
          10          446          112           62            4           57 
TCGA-SX-A7SS 
        1247 

$`DEL PEAK  4(4Q34.3) WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         554          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
          49            2          780          729          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
         118            4         1778         1636          412          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
         763         1357           67          595          659          747 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 
         108          510           14         1029          930          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
          85         1536          857          803          627           14 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
          35          460         1338          671           64          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
         207            5          102          167           52         2639 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 
         792          771          403           29          364         3760 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        2948         2839         1864         1533         1516          799 
TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
         612          232          214          218          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         414         3950         1093         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 
         114          445           92         1240         2460         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY 
        1670         1040          578          757            7           36 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
         208         1575         1479         1194         1059          765 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
         786          279         1967         5925          393          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          32          178           91         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 
        1726          167          511          608          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
         146            2          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         148         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
         174         1079         1199          994          508          423 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SU TCGA-Y8-A894 
        1973          102          925          494          847          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
           2          186          181          205 

  DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE 
                            4                             2 
  DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE 
                         2429                          5925 
  DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE 
                        112.0                         548.5 
[1] "4.0 - 2429.0 (112.0)" "2.0 - 5925.0 (548.5)"
[1] "hr=" "5.7"
D11V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  4(4Q34.3) MUTATED         6        2        14        2
  DEL PEAK  4(4Q34.3) WILD-TYPE     116        9        28       10
D11V3, multiclass
           clus
vv          DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE
  STAGE I                             6                           116
  STAGE II                            2                             9
  STAGE III                          14                            28
  STAGE IV                            2                            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                             T1  T2 T3+T4
  DEL PEAK  4(4Q34.3) MUTATED     7   4    13
  DEL PEAK  4(4Q34.3) WILD-TYPE 123  14    37
D11V4, multiclass
       clus
vv      DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE
  T1                              7                           123
  T2                              4                            14
  T3+T4                          13                            37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  4(4Q34.3) MUTATED    5  8  0
  DEL PEAK  4(4Q34.3) WILD-TYPE 28 12  4
D11V5, multiclass
    clus
vv   DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE
  N0                           5                            28
  N1                           8                            12
  N2                           0                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  DEL PEAK  4(4Q34.3) MUTATED   10  2 12
  DEL PEAK  4(4Q34.3) WILD-TYPE 71  6 84
D11V6, multiclass
    clus
vv   DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE
  M0                          10                            71
  M1                           2                             6
  MX                          12                            84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(4Q34.3) MUTATED    13  11
  DEL PEAK  4(4Q34.3) WILD-TYPE  45 129
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(4Q34.3) MUTATED     13   11
  DEL PEAK  4(4Q34.3) WILD-TYPE   45  129
        clus
vv       DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE
  FEMALE                          13                            45
  MALE                            11                           129
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, continuous
[1] "Remove cluster labels:"      "DEL PEAK  4(4Q34.3) MUTATED"
clus
  DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE 
                            2                            22 
                   TCGA-A4-A48D                    TCGA-B1-A654 
"DEL PEAK  4(4Q34.3) WILD-TYPE" "DEL PEAK  4(4Q34.3) WILD-TYPE" 
                   TCGA-B9-A44B                    TCGA-B9-A69E 
"DEL PEAK  4(4Q34.3) WILD-TYPE" "DEL PEAK  4(4Q34.3) WILD-TYPE" 
                   TCGA-G7-A8LD                    TCGA-GL-7773 
"DEL PEAK  4(4Q34.3) WILD-TYPE" "DEL PEAK  4(4Q34.3) WILD-TYPE" 
                   TCGA-GL-A59T                    TCGA-HE-A5NI 
"DEL PEAK  4(4Q34.3) WILD-TYPE" "DEL PEAK  4(4Q34.3) WILD-TYPE" 
                   TCGA-HE-A5NJ                    TCGA-IA-A40U 
"DEL PEAK  4(4Q34.3) WILD-TYPE" "DEL PEAK  4(4Q34.3) WILD-TYPE" 
                   TCGA-MH-A854                    TCGA-MH-A856 
"DEL PEAK  4(4Q34.3) WILD-TYPE" "DEL PEAK  4(4Q34.3) WILD-TYPE" 
                   TCGA-P4-A5E7                    TCGA-P4-A5EB 
"DEL PEAK  4(4Q34.3) WILD-TYPE" "DEL PEAK  4(4Q34.3) WILD-TYPE" 
                   TCGA-PJ-A5Z9                    TCGA-SX-A71S 
"DEL PEAK  4(4Q34.3) WILD-TYPE" "DEL PEAK  4(4Q34.3) WILD-TYPE" 
                   TCGA-SX-A71U                    TCGA-SX-A7SL 
"DEL PEAK  4(4Q34.3) WILD-TYPE" "DEL PEAK  4(4Q34.3) WILD-TYPE" 
                   TCGA-SX-A7SM                    TCGA-Y8-A894 
"DEL PEAK  4(4Q34.3) WILD-TYPE" "DEL PEAK  4(4Q34.3) WILD-TYPE" 
                   TCGA-Y8-A896                    TCGA-Y8-A8RZ 
"DEL PEAK  4(4Q34.3) WILD-TYPE" "DEL PEAK  4(4Q34.3) WILD-TYPE" 
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(4Q34.3) MUTATED                                  0     2
  DEL PEAK  4(4Q34.3) WILD-TYPE                                2     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(4Q34.3) MUTATED                           5    14
  DEL PEAK  4(4Q34.3) WILD-TYPE                        44   115
D11V10, multiclass
                                  clus
vv                                 DEL PEAK  4(4Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     14
                                  clus
vv                                 DEL PEAK  4(4Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   44
  WHITE                                                      115
[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"
D11V11, binary
                               cls
clus                              0   1
  DEL PEAK  4(4Q34.3) MUTATED     1  18
  DEL PEAK  4(4Q34.3) WILD-TYPE   8 135
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(4Q34.3) MUTATED      1   18
  DEL PEAK  4(4Q34.3) WILD-TYPE    8  135
                        clus
vv                       DEL PEAK  4(4Q34.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          18
                        clus
vv                       DEL PEAK  4(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           135
[1] 2 2
[1] FALSE

Clustering(12) Variable = DEL PEAK  5(5P14.2) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(5P14.2) MUTATED     5   1
  DEL PEAK  5(5P14.2) WILD-TYPE 161   6
  DEL PEAK  5(5P14.2) MUTATED DEL PEAK  5(5P14.2) WILD-TYPE 
                            6                           167 
  DEL PEAK  5(5P14.2) MUTATED DEL PEAK  5(5P14.2) WILD-TYPE 
                            1                             6 
$`DEL PEAK  5(5P14.2) MUTATED`
TCGA-A4-7286 TCGA-A4-7997 TCGA-BQ-5878 TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-Q2-A5QZ 
         554            2         1938           84           97           57 

$`DEL PEAK  5(5P14.2) WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
          21          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
          49          140          780          729          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
         118           87            4         1778         1636          412 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         223          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          857          803          627           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         460         1338          671           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
           5          102          167           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
         270         1454         1242          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 
         771          403          233           29          364         3760 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        2948         2839         1864         1533         1516          799 
TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
         612          232          214          218          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         414         3950         1093         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         114          445           92         1240         2429         2460 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 
        1856         1670         1040          578          757           10 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
           7           36          208         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD 
        1059          765          446          786          279         1967 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         511          608           62          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
           2            4          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         148         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
         174         1079         1199          994          508          423 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU 
        1973          102          925          494         1247          847 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         224            2          186          181          205 

  DEL PEAK  5(5P14.2) MUTATED DEL PEAK  5(5P14.2) WILD-TYPE 
                            2                             2 
  DEL PEAK  5(5P14.2) MUTATED DEL PEAK  5(5P14.2) WILD-TYPE 
                         1938                          5925 
  DEL PEAK  5(5P14.2) MUTATED DEL PEAK  5(5P14.2) WILD-TYPE 
                         90.5                         510.0 
[1] "2.0 - 1938.0 (90.5)"  "2.0 - 5925.0 (510.0)"
[1] "hr=" "11" 
D12V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  5(5P14.2) MUTATED         2        0         5        2
  DEL PEAK  5(5P14.2) WILD-TYPE     120       11        37       10
D12V3, multiclass
           clus
vv          DEL PEAK  5(5P14.2) MUTATED DEL PEAK  5(5P14.2) WILD-TYPE
  STAGE I                             2                           120
  STAGE II                            0                            11
  STAGE III                           5                            37
  STAGE IV                            2                            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                             T1  T2 T3+T4
  DEL PEAK  5(5P14.2) MUTATED     1   1     8
  DEL PEAK  5(5P14.2) WILD-TYPE 129  17    42
D12V4, multiclass
       clus
vv      DEL PEAK  5(5P14.2) MUTATED DEL PEAK  5(5P14.2) WILD-TYPE
  T1                              1                           129
  T2                              1                            17
  T3+T4                           8                            42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  5(5P14.2) MUTATED    0  4  1
  DEL PEAK  5(5P14.2) WILD-TYPE 33 16  3
D12V5, multiclass
    clus
vv   DEL PEAK  5(5P14.2) MUTATED DEL PEAK  5(5P14.2) WILD-TYPE
  N0                           0                            33
  N1                           4                            16
  N2                           1                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  DEL PEAK  5(5P14.2) MUTATED    4  1  4
  DEL PEAK  5(5P14.2) WILD-TYPE 77  7 92
D12V6, multiclass
    clus
vv   DEL PEAK  5(5P14.2) MUTATED DEL PEAK  5(5P14.2) WILD-TYPE
  M0                           4                            77
  M1                           1                             7
  MX                           4                            92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(5P14.2) MUTATED     6   4
  DEL PEAK  5(5P14.2) WILD-TYPE  52 136
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(5P14.2) MUTATED      6    4
  DEL PEAK  5(5P14.2) WILD-TYPE   52  136
        clus
vv       DEL PEAK  5(5P14.2) MUTATED DEL PEAK  5(5P14.2) WILD-TYPE
  FEMALE                           6                            52
  MALE                             4                           136
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
[1] "Remove cluster labels:"      "DEL PEAK  5(5P14.2) MUTATED"
clus
  DEL PEAK  5(5P14.2) MUTATED DEL PEAK  5(5P14.2) WILD-TYPE 
                            1                            23 
                   TCGA-A4-A48D                    TCGA-B1-A654 
"DEL PEAK  5(5P14.2) WILD-TYPE" "DEL PEAK  5(5P14.2) WILD-TYPE" 
                   TCGA-B9-A44B                    TCGA-B9-A69E 
"DEL PEAK  5(5P14.2) WILD-TYPE" "DEL PEAK  5(5P14.2) WILD-TYPE" 
                   TCGA-G7-A8LD                    TCGA-GL-7773 
"DEL PEAK  5(5P14.2) WILD-TYPE" "DEL PEAK  5(5P14.2) WILD-TYPE" 
                   TCGA-GL-A59T                    TCGA-HE-A5NI 
"DEL PEAK  5(5P14.2) WILD-TYPE" "DEL PEAK  5(5P14.2) WILD-TYPE" 
                   TCGA-HE-A5NJ                    TCGA-IA-A40U 
"DEL PEAK  5(5P14.2) WILD-TYPE" "DEL PEAK  5(5P14.2) WILD-TYPE" 
                   TCGA-MH-A854                    TCGA-MH-A856 
"DEL PEAK  5(5P14.2) WILD-TYPE" "DEL PEAK  5(5P14.2) WILD-TYPE" 
                   TCGA-P4-A5E7                    TCGA-P4-A5EB 
"DEL PEAK  5(5P14.2) WILD-TYPE" "DEL PEAK  5(5P14.2) WILD-TYPE" 
                   TCGA-PJ-A5Z9                    TCGA-SX-A71S 
"DEL PEAK  5(5P14.2) WILD-TYPE" "DEL PEAK  5(5P14.2) WILD-TYPE" 
                   TCGA-SX-A71U                    TCGA-SX-A7SL 
"DEL PEAK  5(5P14.2) WILD-TYPE" "DEL PEAK  5(5P14.2) WILD-TYPE" 
                   TCGA-SX-A7SM                    TCGA-SX-A7SS 
"DEL PEAK  5(5P14.2) WILD-TYPE" "DEL PEAK  5(5P14.2) WILD-TYPE" 
                   TCGA-Y8-A894                    TCGA-Y8-A896 
"DEL PEAK  5(5P14.2) WILD-TYPE" "DEL PEAK  5(5P14.2) WILD-TYPE" 
                   TCGA-Y8-A8RZ 
"DEL PEAK  5(5P14.2) WILD-TYPE" 
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(5P14.2) MUTATED                                  0     0
  DEL PEAK  5(5P14.2) WILD-TYPE                                2     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(5P14.2) MUTATED                           2     6
  DEL PEAK  5(5P14.2) WILD-TYPE                        47   123
D12V10, multiclass
                                  clus
vv                                 DEL PEAK  5(5P14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                      6
                                  clus
vv                                 DEL PEAK  5(5P14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   47
  WHITE                                                      123
[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"
D12V11, binary
                               cls
clus                              0   1
  DEL PEAK  5(5P14.2) MUTATED     1   5
  DEL PEAK  5(5P14.2) WILD-TYPE   8 148
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(5P14.2) MUTATED      1    5
  DEL PEAK  5(5P14.2) WILD-TYPE    8  148
                        clus
vv                       DEL PEAK  5(5P14.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           5
                        clus
vv                       DEL PEAK  5(5P14.2) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           148
[1] 2 2
[1] FALSE

Clustering(13) Variable = DEL PEAK  6(5Q35.2) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(5Q35.2) MUTATED     7   1
  DEL PEAK  6(5Q35.2) WILD-TYPE 159   6
  DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE 
                            8                           165 
  DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE 
                            1                             6 
$`DEL PEAK  6(5Q35.2) MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-AL-A5DJ TCGA-B3-4104 TCGA-BQ-5894 TCGA-DZ-6131 
         554           21           26         1049           84         2429 
TCGA-F9-A4JJ TCGA-GL-7966 
          97          112 

$`DEL PEAK  6(5Q35.2) WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
         493            3          582           27            7           49 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
           2          140          780          729          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
         118           87            4         1778         1636          412 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
         923          763         1357           67          595          223 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         659          747          108          510           14         1029 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         307          930          379           85         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
         671           64          585          207            5          102 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
         167           52         2639          586          270         1938 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
        1454         1242          792          921          792          771 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 
         403          233           29          364         3760         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2839         1864         1533         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
         445           92         1240         2460         1856         1670 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
        1040          578          757           10            7           36 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
         208         1575         1479         1194         1059          765 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 
         446          786          279         1967         5925          393 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
         841           32          178           91         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
         360         1726          167          511          608           62 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
         677          649          146            2            4          160 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          391          543          438 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         292           11          541          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
        2584         2816          391          174           57         1079 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1199          994          508          423         1973          102 
TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 
         925          494         1247          847          224            2 
TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         186          181          205 

  DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE 
                           21                             2 
  DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE 
                         2429                          5925 
  DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE 
                        104.5                         510.0 
[1] "21.0 - 2429.0 (104.5)" "2.0 - 5925.0 (510.0)" 
[1] "hr=" "3.8"
D13V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  6(5Q35.2) MUTATED         1        1         7        1
  DEL PEAK  6(5Q35.2) WILD-TYPE     121       10        35       11
D13V3, multiclass
           clus
vv          DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE
  STAGE I                             1                           121
  STAGE II                            1                            10
  STAGE III                           7                            35
  STAGE IV                            1                            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                             T1  T2 T3+T4
  DEL PEAK  6(5Q35.2) MUTATED     1   1     9
  DEL PEAK  6(5Q35.2) WILD-TYPE 129  17    41
D13V4, multiclass
       clus
vv      DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE
  T1                              1                           129
  T2                              1                            17
  T3+T4                           9                            41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  6(5Q35.2) MUTATED    1  4  0
  DEL PEAK  6(5Q35.2) WILD-TYPE 32 16  4
D13V5, multiclass
    clus
vv   DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE
  N0                           1                            32
  N1                           4                            16
  N2                           0                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  DEL PEAK  6(5Q35.2) MUTATED    3  1  6
  DEL PEAK  6(5Q35.2) WILD-TYPE 78  7 90
D13V6, multiclass
    clus
vv   DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE
  M0                           3                            78
  M1                           1                             7
  MX                           6                            90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(5Q35.2) MUTATED     7   4
  DEL PEAK  6(5Q35.2) WILD-TYPE  51 136
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(5Q35.2) MUTATED      7    4
  DEL PEAK  6(5Q35.2) WILD-TYPE   51  136
        clus
vv       DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE
  FEMALE                           7                            51
  MALE                             4                           136
[1] 2 2
[1] FALSE
D13V8, continuous
[1] "Remove cluster labels:"      "DEL PEAK  6(5Q35.2) MUTATED"
clus
  DEL PEAK  6(5Q35.2) MUTATED DEL PEAK  6(5Q35.2) WILD-TYPE 
                            1                            51 
                   TCGA-A4-7828                    TCGA-A4-8310 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-A4-8311                    TCGA-A4-8312 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-A4-8518                    TCGA-A4-8630 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-A4-A4ZT                    TCGA-A4-A57E 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-A4-A5DU                    TCGA-A4-A5XZ 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-A4-A6HP                    TCGA-AL-3466 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-DW-5560                    TCGA-DW-5561 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-DW-7834                    TCGA-DW-7836 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-DW-7837                    TCGA-DW-7838 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-DW-7839                    TCGA-DW-7840 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-DW-7841                    TCGA-DW-7842 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-DW-7963                    TCGA-EV-5901 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-EV-5902                    TCGA-EV-5903 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-G7-6790                    TCGA-G7-6793 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-G7-6796                    TCGA-G7-6797 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-G7-7501                    TCGA-G7-7502 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-G7-A4TM                    TCGA-G7-A8LD 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-IA-A40U                    TCGA-IA-A40X 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-IA-A40Y                    TCGA-J7-8537 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-Q2-A5QZ                    TCGA-SX-A71R 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A71S                    TCGA-SX-A71U 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A71V                    TCGA-SX-A7SL 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A7SM                    TCGA-SX-A7SN 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A7SO                    TCGA-SX-A7SP 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A7SQ                    TCGA-SX-A7SS 
"DEL PEAK  6(5Q35.2) WILD-TYPE" "DEL PEAK  6(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A7SU 
"DEL PEAK  6(5Q35.2) WILD-TYPE" 
D13V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(5Q35.2) MUTATED                                  0     0
  DEL PEAK  6(5Q35.2) WILD-TYPE                                2     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(5Q35.2) MUTATED                           1     8
  DEL PEAK  6(5Q35.2) WILD-TYPE                        48   121
D13V10, multiclass
                                  clus
vv                                 DEL PEAK  6(5Q35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                      8
                                  clus
vv                                 DEL PEAK  6(5Q35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   48
  WHITE                                                      121
[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"
D13V11, binary
                               cls
clus                              0   1
  DEL PEAK  6(5Q35.2) MUTATED     1   6
  DEL PEAK  6(5Q35.2) WILD-TYPE   8 147
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(5Q35.2) MUTATED      1    6
  DEL PEAK  6(5Q35.2) WILD-TYPE    8  147
                        clus
vv                       DEL PEAK  6(5Q35.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           6
                        clus
vv                       DEL PEAK  6(5Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           147
[1] 2 2
[1] FALSE

Clustering(14) Variable = DEL PEAK  7(6P12.3) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(6P12.3) MUTATED    13   1
  DEL PEAK  7(6P12.3) WILD-TYPE 153   6
  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                           14                           159 
  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                            1                             6 
$`DEL PEAK  7(6P12.3) MUTATED`
TCGA-A4-7286 TCGA-AL-A5DJ TCGA-B3-3926 TCGA-B9-A44B TCGA-BQ-5890 TCGA-BQ-7048 
         554           26          307           64          233         2839 
TCGA-BQ-7056 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6797 TCGA-G7-7502 
         612          578           10          208          765          786 
TCGA-SX-A7SL TCGA-Y8-A896 
         423          186 

$`DEL PEAK  7(6P12.3) WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
          21          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
         412          923          763         1357           67          595 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         223          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
        1029          930         1049          379           85         1536 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
         857          803          627           14           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1338          671          585          207            5          102 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
         167           52         2639          586          270         1938 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
        1454         1242          792          921          792          771 
TCGA-BQ-5888 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 
         403           29          364           84         3760         2948 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 
        1864         1533         1516          799          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         218          116          353          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1240         2429         2460         1856         1670         1040 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 
         757           97            7           36         1575         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 
        1194         1059          446          279         1967         5925 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
         393          112          841           32          178           91 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
        2072          408          360         1726          167          511 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         608           62          677          649          146            2 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
           4          160          885          161         1043          391 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
         543          438          292           11          541          148 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3035         2653         2584         2816          391          174 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM 
          57         1079         1199          994          508         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 
         102          925          494         1247          847          224 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
           2          181          205 

  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                           10                             2 
  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                         2839                          5925 
  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                          365                           510 
[1] "10.0 - 2839.0 (365.0)" "2.0 - 5925.0 (510.0)" 
[1] "hr=" "2.2"
D14V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  7(6P12.3) MUTATED         5        0        10        2
  DEL PEAK  7(6P12.3) WILD-TYPE     117       11        32       10
D14V3, multiclass
           clus
vv          DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE
  STAGE I                             5                           117
  STAGE II                            0                            11
  STAGE III                          10                            32
  STAGE IV                            2                            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                             T1  T2 T3+T4
  DEL PEAK  7(6P12.3) MUTATED     6   1    11
  DEL PEAK  7(6P12.3) WILD-TYPE 124  17    39
D14V4, multiclass
       clus
vv      DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE
  T1                              6                           124
  T2                              1                            17
  T3+T4                          11                            39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  7(6P12.3) MUTATED    4  1  2
  DEL PEAK  7(6P12.3) WILD-TYPE 29 19  2
D14V5, multiclass
    clus
vv   DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE
  N0                           4                            29
  N1                           1                            19
  N2                           2                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  DEL PEAK  7(6P12.3) MUTATED   10  0  6
  DEL PEAK  7(6P12.3) WILD-TYPE 71  8 90
D14V6, multiclass
    clus
vv   DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE
  M0                          10                            71
  M1                           0                             8
  MX                           6                            90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(6P12.3) MUTATED     7  11
  DEL PEAK  7(6P12.3) WILD-TYPE  51 129
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(6P12.3) MUTATED      7   11
  DEL PEAK  7(6P12.3) WILD-TYPE   51  129
        clus
vv       DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE
  FEMALE                           7                            51
  MALE                            11                           129
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(6P12.3) MUTATED                                  0     1
  DEL PEAK  7(6P12.3) WILD-TYPE                                2     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(6P12.3) MUTATED                           1    13
  DEL PEAK  7(6P12.3) WILD-TYPE                        48   116
D14V10, multiclass
                                  clus
vv                                 DEL PEAK  7(6P12.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     13
                                  clus
vv                                 DEL PEAK  7(6P12.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   48
  WHITE                                                      116
[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"
D14V11, binary
                               cls
clus                              0   1
  DEL PEAK  7(6P12.3) MUTATED     0  14
  DEL PEAK  7(6P12.3) WILD-TYPE   9 139
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(6P12.3) MUTATED      0   14
  DEL PEAK  7(6P12.3) WILD-TYPE    9  139
                        clus
vv                       DEL PEAK  7(6P12.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          14
                        clus
vv                       DEL PEAK  7(6P12.3) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           139
[1] 2 2
[1] FALSE

Clustering(15) Variable = DEL PEAK  8(6Q22.31) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  8(6Q22.31) MUTATED    15   1
  DEL PEAK  8(6Q22.31) WILD-TYPE 151   6
  DEL PEAK  8(6Q22.31) MUTATED DEL PEAK  8(6Q22.31) WILD-TYPE 
                            16                            157 
  DEL PEAK  8(6Q22.31) MUTATED DEL PEAK  8(6Q22.31) WILD-TYPE 
                             1                              6 
$`DEL PEAK  8(6Q22.31) MUTATED`
TCGA-A4-7286 TCGA-B3-3926 TCGA-B9-A44B TCGA-BQ-5875 TCGA-BQ-5888 TCGA-BQ-7056 
         554          307           64         2639          403          612 
TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-7502 TCGA-GL-7966 TCGA-J7-8537 
         578           10          208          786          112            4 
TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A7SL TCGA-Y8-A896 
        2584           57          423          186 

$`DEL PEAK  8(6Q22.31) WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
          21          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
         412          923          763         1357           26           67 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
         595          223          659          747          108          510 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
          14         1029          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          857          803          627           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
         460         1338          671          585          207            5 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
         102          167           52          586          270         1938 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
        1454         1242          792          921          792          771 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 
         233           29          364           84         3760         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 
        2839         1864         1533         1516          799          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        1093         1142          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
          92         1240         2429         2460         1856         1670 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 
        1040          757           97            7           36         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM 
        1479         1194         1059          765          446          279 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        1967         5925          393          841           32          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         511          608           62          677          649          146 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
           2          160          885          161         1043          391 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
         543          438          292           11          541          148 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R 
        3035         2653         2816          391          174         1079 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1199          994          508         1973          102          925 
TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A898 
         494         1247          847          224            2          181 
TCGA-Y8-A8RZ 
         205 

  DEL PEAK  8(6Q22.31) MUTATED DEL PEAK  8(6Q22.31) WILD-TYPE 
                             4                              2 
  DEL PEAK  8(6Q22.31) MUTATED DEL PEAK  8(6Q22.31) WILD-TYPE 
                          2639                           5925 
  DEL PEAK  8(6Q22.31) MUTATED DEL PEAK  8(6Q22.31) WILD-TYPE 
                           355                            511 
[1] "4.0 - 2639.0 (355.0)" "2.0 - 5925.0 (511.0)"
[1] "hr=" "1.5"
D15V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  8(6Q22.31) MUTATED         7        0         9        3
  DEL PEAK  8(6Q22.31) WILD-TYPE     115       11        33        9
D15V3, multiclass
           clus
vv          DEL PEAK  8(6Q22.31) MUTATED DEL PEAK  8(6Q22.31) WILD-TYPE
  STAGE I                              7                            115
  STAGE II                             0                             11
  STAGE III                            9                             33
  STAGE IV                             3                              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                              T1  T2 T3+T4
  DEL PEAK  8(6Q22.31) MUTATED     7   0    13
  DEL PEAK  8(6Q22.31) WILD-TYPE 123  18    37
D15V4, multiclass
       clus
vv      DEL PEAK  8(6Q22.31) MUTATED DEL PEAK  8(6Q22.31) WILD-TYPE
  T1                               7                            123
  T2                               0                             18
  T3+T4                           13                             37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK  8(6Q22.31) MUTATED    3  3  2
  DEL PEAK  8(6Q22.31) WILD-TYPE 30 17  2
D15V5, multiclass
    clus
vv   DEL PEAK  8(6Q22.31) MUTATED DEL PEAK  8(6Q22.31) WILD-TYPE
  N0                            3                             30
  N1                            3                             17
  N2                            2                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK  8(6Q22.31) MUTATED   10  1  7
  DEL PEAK  8(6Q22.31) WILD-TYPE 71  7 89
D15V6, multiclass
    clus
vv   DEL PEAK  8(6Q22.31) MUTATED DEL PEAK  8(6Q22.31) WILD-TYPE
  M0                           10                             71
  M1                            1                              7
  MX                            7                             89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                                cls
clus                               0   1
  DEL PEAK  8(6Q22.31) MUTATED    11   9
  DEL PEAK  8(6Q22.31) WILD-TYPE  47 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(6Q22.31) MUTATED     11    9
  DEL PEAK  8(6Q22.31) WILD-TYPE   47  131
        clus
vv       DEL PEAK  8(6Q22.31) MUTATED DEL PEAK  8(6Q22.31) WILD-TYPE
  FEMALE                           11                             47
  MALE                              9                            131
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(6Q22.31) MUTATED                                  0     2
  DEL PEAK  8(6Q22.31) WILD-TYPE                                2     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(6Q22.31) MUTATED                           2    13
  DEL PEAK  8(6Q22.31) WILD-TYPE                        47   116
D15V10, multiclass
                                  clus
vv                                 DEL PEAK  8(6Q22.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      13
                                  clus
vv                                 DEL PEAK  8(6Q22.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    47
  WHITE                                                       116
[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"
D15V11, binary
                                cls
clus                               0   1
  DEL PEAK  8(6Q22.31) MUTATED     0  14
  DEL PEAK  8(6Q22.31) WILD-TYPE   9 139
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(6Q22.31) MUTATED      0   14
  DEL PEAK  8(6Q22.31) WILD-TYPE    9  139
                        clus
vv                       DEL PEAK  8(6Q22.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           14
                        clus
vv                       DEL PEAK  8(6Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            139
[1] 2 2
[1] FALSE

Clustering(16) Variable = DEL PEAK  9(6Q27) MUTATION ANALYSIS
D16V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  9(6Q27) MUTATED    18   2
  DEL PEAK  9(6Q27) WILD-TYPE 148   5
  DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE 
                         20                         153 
  DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE 
                          2                           5 
$`DEL PEAK  9(6Q27) MUTATED`
TCGA-A4-7286 TCGA-AL-A5DJ TCGA-B3-3926 TCGA-B9-A44B TCGA-BQ-5875 TCGA-BQ-5888 
         554           26          307           64         2639          403 
TCGA-BQ-5890 TCGA-BQ-7056 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-7502 
         233          612          578           10          208          786 
TCGA-G7-A8LD TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5EB TCGA-Q2-A5QZ 
        1967          112           62            4         2584           57 
TCGA-SX-A7SL TCGA-Y8-A896 
         423          186 

$`DEL PEAK  9(6Q27) WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
          21          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
           2          118           87            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
         412          923          763         1357           67          595 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         223          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
        1029          930         1049          379           85         1536 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
         857          803          627           14           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1338          671          585          207            5          102 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 
         167           52          586          270         1938         1454 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5891 
        1242          792          921          792          771           29 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
         364           84         3760         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1533         1516          799          232          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
         116          353          414         3950         1093         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          445           92         1240 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 
        2429         2460         1856         1670         1040          757 
TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
          97            7           36         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
        1059          765          446          279         5925          393 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
         841           32          178           91         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 
         360         1726          167          511          608          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         649          146            2          160          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          391          543          438          292           11 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 
         541          148         3035         2653         2816          391 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM 
         174         1079         1199          994          508         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 
         102          925          494         1247          847          224 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
           2          181          205 

  DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE 
                          4                           2 
  DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE 
                       2639                        5925 
  DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE 
                        270                         516 
[1] "4.0 - 2639.0 (270.0)" "2.0 - 5925.0 (516.0)"
[1] "hr=" "2.9"
D16V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  9(6Q27) MUTATED         7        0        13        2
  DEL PEAK  9(6Q27) WILD-TYPE     115       11        29       10
D16V3, multiclass
           clus
vv          DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE
  STAGE I                           7                         115
  STAGE II                          0                          11
  STAGE III                        13                          29
  STAGE IV                          2                          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                           T1  T2 T3+T4
  DEL PEAK  9(6Q27) MUTATED     7   0    16
  DEL PEAK  9(6Q27) WILD-TYPE 123  18    34
D16V4, multiclass
       clus
vv      DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE
  T1                            7                         123
  T2                            0                          18
  T3+T4                        16                          34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2
  DEL PEAK  9(6Q27) MUTATED    4  4  2
  DEL PEAK  9(6Q27) WILD-TYPE 29 16  2
D16V5, multiclass
    clus
vv   DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE
  N0                         4                          29
  N1                         4                          16
  N2                         2                           2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          M0 M1 MX
  DEL PEAK  9(6Q27) MUTATED   11  0 10
  DEL PEAK  9(6Q27) WILD-TYPE 70  8 86
D16V6, multiclass
    clus
vv   DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE
  M0                        11                          70
  M1                         0                           8
  MX                        10                          86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                             cls
clus                            0   1
  DEL PEAK  9(6Q27) MUTATED    13  10
  DEL PEAK  9(6Q27) WILD-TYPE  45 130
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(6Q27) MUTATED     13   10
  DEL PEAK  9(6Q27) WILD-TYPE   45  130
        clus
vv       DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE
  FEMALE                        13                          45
  MALE                          10                         130
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(6Q27) MUTATED                                  0     2
  DEL PEAK  9(6Q27) WILD-TYPE                                2     2
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(6Q27) MUTATED                           2    16
  DEL PEAK  9(6Q27) WILD-TYPE                        47   113
D16V10, multiclass
                                  clus
vv                                 DEL PEAK  9(6Q27) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    2
  BLACK OR AFRICAN AMERICAN                                2
  WHITE                                                   16
                                  clus
vv                                 DEL PEAK  9(6Q27) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 47
  WHITE                                                    113
[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"
D16V11, binary
                             cls
clus                            0   1
  DEL PEAK  9(6Q27) MUTATED     0  17
  DEL PEAK  9(6Q27) WILD-TYPE   9 136
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(6Q27) MUTATED      0   17
  DEL PEAK  9(6Q27) WILD-TYPE    9  136
                        clus
vv                       DEL PEAK  9(6Q27) MUTATED DEL PEAK  9(6Q27) WILD-TYPE
  HISPANIC OR LATINO                             0                           9
  NOT HISPANIC OR LATINO                        17                         136
[1] 2 2
[1] FALSE

Clustering(17) Variable = DEL PEAK 10(9P21.3) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(9P21.3) MUTATED    18   4
  DEL PEAK 10(9P21.3) WILD-TYPE 148   3
  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                           22                           151 
  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                            4                             3 
$`DEL PEAK 10(9P21.3) MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B3-3926 TCGA-B9-4116 
         554           21           87           26          307          627 
TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5888 TCGA-BQ-7048 TCGA-BQ-7056 TCGA-DZ-6131 
         102          270          403         2839          612         2429 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7966 
          10          208         1059          446         1967          112 
TCGA-IA-A40Y TCGA-J7-8537 TCGA-SX-A71V TCGA-Y8-A896 
          62            4          508          186 

$`DEL PEAK 10(9P21.3) WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
         493            3          582           27            7           49 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
           2          140          780          729          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
         118            4         1778         1636          412          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
         763         1357           67          595          223          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 
         747          108          510           14         1029          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379           85         1536          857          803 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
          14           35          460         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
         585          207            5          167           52         2639 
TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         586         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
         792          771          233           29          364           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        3760         2948         1864         1533         1516          799 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
         445           92         1240         2460         1856         1670 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY 
        1040          578          757           97            7           36 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM 
        1575         1479         1194          765          786          279 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
        5925          393          841           32          178           91 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
        2072          408          360         1726          167          511 
TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
         608          677          649          146            2          160 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          391          543          438 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         292           11          541          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
        2584         2816          391          174           57         1079 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1199          994          423         1973          102          925 
TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A898 
         494         1247          847          224            2          181 
TCGA-Y8-A8RZ 
         205 

  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                            4                             2 
  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                         2839                          5925 
  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                        288.5                         541.0 
[1] "4.0 - 2839.0 (288.5)" "2.0 - 5925.0 (541.0)"
[1] "hr=" "9.1"
D17V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 10(9P21.3) MUTATED         6        0        15        6
  DEL PEAK 10(9P21.3) WILD-TYPE     116       11        27        6
D17V3, multiclass
           clus
vv          DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE
  STAGE I                             6                           116
  STAGE II                            0                            11
  STAGE III                          15                            27
  STAGE IV                            6                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2 T3+T4
  DEL PEAK 10(9P21.3) MUTATED     7   2    20
  DEL PEAK 10(9P21.3) WILD-TYPE 123  16    30
D17V4, multiclass
       clus
vv      DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE
  T1                              7                           123
  T2                              2                            16
  T3+T4                          20                            30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK 10(9P21.3) MUTATED    5 11  2
  DEL PEAK 10(9P21.3) WILD-TYPE 28  9  2
D17V5, multiclass
    clus
vv   DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE
  N0                           5                            28
  N1                          11                             9
  N2                           2                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  DEL PEAK 10(9P21.3) MUTATED    9  4 13
  DEL PEAK 10(9P21.3) WILD-TYPE 72  4 83
D17V6, multiclass
    clus
vv   DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE
  M0                           9                            72
  M1                           4                             4
  MX                          13                            83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(9P21.3) MUTATED    16  13
  DEL PEAK 10(9P21.3) WILD-TYPE  42 127
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(9P21.3) MUTATED     16   13
  DEL PEAK 10(9P21.3) WILD-TYPE   42  127
        clus
vv       DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE
  FEMALE                          16                            42
  MALE                            13                           127
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(9P21.3) MUTATED                                  0     2
  DEL PEAK 10(9P21.3) WILD-TYPE                                2     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(9P21.3) MUTATED                           3    23
  DEL PEAK 10(9P21.3) WILD-TYPE                        46   106
D17V10, multiclass
                                  clus
vv                                 DEL PEAK 10(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                     23
                                  clus
vv                                 DEL PEAK 10(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   46
  WHITE                                                      106
[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"
D17V11, binary
                               cls
clus                              0   1
  DEL PEAK 10(9P21.3) MUTATED     0  24
  DEL PEAK 10(9P21.3) WILD-TYPE   9 129
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(9P21.3) MUTATED      0   24
  DEL PEAK 10(9P21.3) WILD-TYPE    9  129
                        clus
vv                       DEL PEAK 10(9P21.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          24
                        clus
vv                       DEL PEAK 10(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           129
[1] 2 2
[1] FALSE

Clustering(18) Variable = DEL PEAK 11(10P11.21) MUTATION ANALYSIS
D18V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 11(10P11.21) MUTATED    10   2
  DEL PEAK 11(10P11.21) WILD-TYPE 156   5
  DEL PEAK 11(10P11.21) MUTATED DEL PEAK 11(10P11.21) WILD-TYPE 
                             12                             161 
  DEL PEAK 11(10P11.21) MUTATED DEL PEAK 11(10P11.21) WILD-TYPE 
                              2                               5 
$`DEL PEAK 11(10P11.21) MUTATED`
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B9-4116 TCGA-B9-A44B TCGA-BQ-5876 TCGA-DZ-6131 
          87           26          627           64          586         2429 
TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-7966 TCGA-J7-8537 TCGA-Q2-A5QZ 
         208          446          786          112            4           57 

$`DEL PEAK 11(10P11.21) WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
         516            2          118            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
         412          923          763         1357           67          595 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         223          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
        1536          857          803           14           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1338          671          585          207            5          102 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 
         167           52         2639          270         1938         1454 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
        1242          792          921          792          771          403 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 
         233           29          364           84         3760         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2839         1864         1533         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
         445           92         1240         2460         1856         1670 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
        1040          578          757           97           10            7 
TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
          36         1575         1479         1194         1059          765 
TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
         279         1967         5925          393          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
         167          511          608           62          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
         146            2          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         148         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
         174         1079         1199          994          508          423 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU 
        1973          102          925          494         1247          847 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         224            2          186          181          205 

  DEL PEAK 11(10P11.21) MUTATED DEL PEAK 11(10P11.21) WILD-TYPE 
                              4                               2 
  DEL PEAK 11(10P11.21) MUTATED DEL PEAK 11(10P11.21) WILD-TYPE 
                           2429                            5925 
  DEL PEAK 11(10P11.21) MUTATED DEL PEAK 11(10P11.21) WILD-TYPE 
                            160                             511 
[1] "4.0 - 2429.0 (160.0)" "2.0 - 5925.0 (511.0)"
[1] "hr=" "7"  
D18V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 11(10P11.21) MUTATED         2        0         8        1
  DEL PEAK 11(10P11.21) WILD-TYPE     120       11        34       11
D18V3, multiclass
           clus
vv          DEL PEAK 11(10P11.21) MUTATED DEL PEAK 11(10P11.21) WILD-TYPE
  STAGE I                               2                             120
  STAGE II                              0                              11
  STAGE III                             8                              34
  STAGE IV                              1                              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                               T1  T2 T3+T4
  DEL PEAK 11(10P11.21) MUTATED     3   1     8
  DEL PEAK 11(10P11.21) WILD-TYPE 127  17    42
D18V4, multiclass
       clus
vv      DEL PEAK 11(10P11.21) MUTATED DEL PEAK 11(10P11.21) WILD-TYPE
  T1                                3                             127
  T2                                1                              17
  T3+T4                             8                              42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2
  DEL PEAK 11(10P11.21) MUTATED    1  4  1
  DEL PEAK 11(10P11.21) WILD-TYPE 32 16  3
D18V5, multiclass
    clus
vv   DEL PEAK 11(10P11.21) MUTATED DEL PEAK 11(10P11.21) WILD-TYPE
  N0                             1                              32
  N1                             4                              16
  N2                             1                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1 MX
  DEL PEAK 11(10P11.21) MUTATED    2  0  8
  DEL PEAK 11(10P11.21) WILD-TYPE 79  8 88
D18V6, multiclass
    clus
vv   DEL PEAK 11(10P11.21) MUTATED DEL PEAK 11(10P11.21) WILD-TYPE
  M0                             2                              79
  M1                             0                               8
  MX                             8                              88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                                 cls
clus                                0   1
  DEL PEAK 11(10P11.21) MUTATED     7   5
  DEL PEAK 11(10P11.21) WILD-TYPE  51 135
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(10P11.21) MUTATED      7    5
  DEL PEAK 11(10P11.21) WILD-TYPE   51  135
        clus
vv       DEL PEAK 11(10P11.21) MUTATED DEL PEAK 11(10P11.21) WILD-TYPE
  FEMALE                             7                              51
  MALE                               5                             135
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
[1] "Remove cluster labels:"        "DEL PEAK 11(10P11.21) MUTATED"
clus
  DEL PEAK 11(10P11.21) MUTATED DEL PEAK 11(10P11.21) WILD-TYPE 
                              2                              22 
                     TCGA-A4-A48D                      TCGA-B1-A654 
"DEL PEAK 11(10P11.21) WILD-TYPE" "DEL PEAK 11(10P11.21) WILD-TYPE" 
                     TCGA-B9-A69E                      TCGA-G7-A8LD 
"DEL PEAK 11(10P11.21) WILD-TYPE" "DEL PEAK 11(10P11.21) WILD-TYPE" 
                     TCGA-GL-7773                      TCGA-GL-A59T 
"DEL PEAK 11(10P11.21) WILD-TYPE" "DEL PEAK 11(10P11.21) WILD-TYPE" 
                     TCGA-HE-A5NI                      TCGA-HE-A5NJ 
"DEL PEAK 11(10P11.21) WILD-TYPE" "DEL PEAK 11(10P11.21) WILD-TYPE" 
                     TCGA-IA-A40U                      TCGA-MH-A854 
"DEL PEAK 11(10P11.21) WILD-TYPE" "DEL PEAK 11(10P11.21) WILD-TYPE" 
                     TCGA-MH-A856                      TCGA-P4-A5E7 
"DEL PEAK 11(10P11.21) WILD-TYPE" "DEL PEAK 11(10P11.21) WILD-TYPE" 
                     TCGA-P4-A5EB                      TCGA-PJ-A5Z9 
"DEL PEAK 11(10P11.21) WILD-TYPE" "DEL PEAK 11(10P11.21) WILD-TYPE" 
                     TCGA-SX-A71S                      TCGA-SX-A71U 
"DEL PEAK 11(10P11.21) WILD-TYPE" "DEL PEAK 11(10P11.21) WILD-TYPE" 
                     TCGA-SX-A7SL                      TCGA-SX-A7SM 
"DEL PEAK 11(10P11.21) WILD-TYPE" "DEL PEAK 11(10P11.21) WILD-TYPE" 
                     TCGA-SX-A7SS                      TCGA-Y8-A894 
"DEL PEAK 11(10P11.21) WILD-TYPE" "DEL PEAK 11(10P11.21) WILD-TYPE" 
                     TCGA-Y8-A896                      TCGA-Y8-A8RZ 
"DEL PEAK 11(10P11.21) WILD-TYPE" "DEL PEAK 11(10P11.21) WILD-TYPE" 
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(10P11.21) MUTATED                                  0     1
  DEL PEAK 11(10P11.21) WILD-TYPE                                2     3
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(10P11.21) MUTATED                           4     7
  DEL PEAK 11(10P11.21) WILD-TYPE                        45   122
D18V10, multiclass
                                  clus
vv                                 DEL PEAK 11(10P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                        7
                                  clus
vv                                 DEL PEAK 11(10P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                          3
  BLACK OR AFRICAN AMERICAN                                     45
  WHITE                                                        122
[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"
D18V11, binary
                                 cls
clus                                0   1
  DEL PEAK 11(10P11.21) MUTATED     0  10
  DEL PEAK 11(10P11.21) WILD-TYPE   9 143
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(10P11.21) MUTATED      0   10
  DEL PEAK 11(10P11.21) WILD-TYPE    9  143
                        clus
vv                       DEL PEAK 11(10P11.21) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            10
                        clus
vv                       DEL PEAK 11(10P11.21) WILD-TYPE
  HISPANIC OR LATINO                                   9
  NOT HISPANIC OR LATINO                             143
[1] 2 2
[1] FALSE

Clustering(19) Variable = DEL PEAK 12(11Q22.3) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 12(11Q22.3) MUTATED    12   4
  DEL PEAK 12(11Q22.3) WILD-TYPE 154   3
  DEL PEAK 12(11Q22.3) MUTATED DEL PEAK 12(11Q22.3) WILD-TYPE 
                            16                            157 
  DEL PEAK 12(11Q22.3) MUTATED DEL PEAK 12(11Q22.3) WILD-TYPE 
                             4                              3 
$`DEL PEAK 12(11Q22.3) MUTATED`
TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B3-4104 TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5877 
          87          223         1049           64          586          270 
TCGA-BQ-5890 TCGA-BQ-7044 TCGA-G7-6789 TCGA-G7-7502 TCGA-G7-A8LD TCGA-IA-A40Y 
         233         3760          208          786         1967           62 
TCGA-J7-8537 TCGA-PJ-A5Z8 TCGA-Y8-A894 TCGA-Y8-A896 
           4          391          224          186 

$`DEL PEAK 12(11Q22.3) WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
         516            2          118            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
         412          923          763         1357           26           67 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         595          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
        1029          307          930          379           85         1536 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
         857          803          627           14           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1338          671          585          207            5          102 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
         167           52         2639         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 
         792          921          792          771          403           29 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
         364           84         2948         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1516          799          612          232          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
         116          353          414         3950         1093         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          445           92         1240 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        2429         2460         1856         1670         1040          578 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 
         757           97           10            7           36         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM 
        1479         1194         1059          765          446          279 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         511          608          677          649          146            2 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         160          885          161         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
         438          292           11          541          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
        2653         2584         2816          174           57         1079 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1199          994          508          423         1973          102 
TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A895 TCGA-Y8-A898 
         925          494         1247          847            2          181 
TCGA-Y8-A8RZ 
         205 

  DEL PEAK 12(11Q22.3) MUTATED DEL PEAK 12(11Q22.3) WILD-TYPE 
                             4                              2 
  DEL PEAK 12(11Q22.3) MUTATED DEL PEAK 12(11Q22.3) WILD-TYPE 
                          3760                           5925 
  DEL PEAK 12(11Q22.3) MUTATED DEL PEAK 12(11Q22.3) WILD-TYPE 
                         228.5                          516.0 
[1] "4.0 - 3760.0 (228.5)" "2.0 - 5925.0 (516.0)"
[1] "hr=" "14" 
D19V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 12(11Q22.3) MUTATED         4        2        10        4
  DEL PEAK 12(11Q22.3) WILD-TYPE     118        9        32        8
D19V3, multiclass
           clus
vv          DEL PEAK 12(11Q22.3) MUTATED DEL PEAK 12(11Q22.3) WILD-TYPE
  STAGE I                              4                            118
  STAGE II                             2                              9
  STAGE III                           10                             32
  STAGE IV                             4                              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                              T1  T2 T3+T4
  DEL PEAK 12(11Q22.3) MUTATED     5   2    13
  DEL PEAK 12(11Q22.3) WILD-TYPE 125  16    37
D19V4, multiclass
       clus
vv      DEL PEAK 12(11Q22.3) MUTATED DEL PEAK 12(11Q22.3) WILD-TYPE
  T1                               5                            125
  T2                               2                             16
  T3+T4                           13                             37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 12(11Q22.3) MUTATED    2  6  2
  DEL PEAK 12(11Q22.3) WILD-TYPE 31 14  2
D19V5, multiclass
    clus
vv   DEL PEAK 12(11Q22.3) MUTATED DEL PEAK 12(11Q22.3) WILD-TYPE
  N0                            2                             31
  N1                            6                             14
  N2                            2                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK 12(11Q22.3) MUTATED    8  2  9
  DEL PEAK 12(11Q22.3) WILD-TYPE 73  6 87
D19V6, multiclass
    clus
vv   DEL PEAK 12(11Q22.3) MUTATED DEL PEAK 12(11Q22.3) WILD-TYPE
  M0                            8                             73
  M1                            2                              6
  MX                            9                             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                                cls
clus                               0   1
  DEL PEAK 12(11Q22.3) MUTATED     8  12
  DEL PEAK 12(11Q22.3) WILD-TYPE  50 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(11Q22.3) MUTATED      8   12
  DEL PEAK 12(11Q22.3) WILD-TYPE   50  128
        clus
vv       DEL PEAK 12(11Q22.3) MUTATED DEL PEAK 12(11Q22.3) WILD-TYPE
  FEMALE                            8                             50
  MALE                             12                            128
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(11Q22.3) MUTATED                                  0     1
  DEL PEAK 12(11Q22.3) WILD-TYPE                                2     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(11Q22.3) MUTATED                           3    14
  DEL PEAK 12(11Q22.3) WILD-TYPE                        46   115
D19V10, multiclass
                                  clus
vv                                 DEL PEAK 12(11Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      14
                                  clus
vv                                 DEL PEAK 12(11Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    46
  WHITE                                                       115
[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"
D19V11, binary
                                cls
clus                               0   1
  DEL PEAK 12(11Q22.3) MUTATED     0  15
  DEL PEAK 12(11Q22.3) WILD-TYPE   9 138
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(11Q22.3) MUTATED      0   15
  DEL PEAK 12(11Q22.3) WILD-TYPE    9  138
                        clus
vv                       DEL PEAK 12(11Q22.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           15
                        clus
vv                       DEL PEAK 12(11Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            138
[1] 2 2
[1] FALSE

Clustering(20) Variable = DEL PEAK 13(11Q24.2) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 13(11Q24.2) MUTATED    11   4
  DEL PEAK 13(11Q24.2) WILD-TYPE 155   3
  DEL PEAK 13(11Q24.2) MUTATED DEL PEAK 13(11Q24.2) WILD-TYPE 
                            15                            158 
  DEL PEAK 13(11Q24.2) MUTATED DEL PEAK 13(11Q24.2) WILD-TYPE 
                             4                              3 
$`DEL PEAK 13(11Q24.2) MUTATED`
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B3-4104 TCGA-B9-A44B TCGA-BQ-5876 
          87           26          223         1049           64          586 
TCGA-BQ-5877 TCGA-BQ-5890 TCGA-BQ-7044 TCGA-G7-6789 TCGA-G7-7502 TCGA-G7-A8LD 
         270          233         3760          208          786         1967 
TCGA-IA-A40Y TCGA-J7-8537 TCGA-Y8-A896 
          62            4          186 

$`DEL PEAK 13(11Q24.2) WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
         516            2          118            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
         412          923          763         1357           67          595 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
         659          747          108          510           14         1029 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         307          930          379           85         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
         671          585          207            5          102          167 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
          52         2639         1938         1454         1242          792 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 TCGA-BQ-5892 
         921          792          771          403           29          364 
TCGA-BQ-5894 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
          84         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         799          612          232          214          218          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         353          414         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
         419          114          445           92         1240         2429 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        2460         1856         1670         1040          578          757 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 
          97           10            7           36         1575         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-GL-6846 
        1194         1059          765          446          279         5925 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
         393          112          841           32          178           91 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
        2072          408          360         1726          167          511 
TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
         608          677          649          146            2          160 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          391          543          438 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         292           11          541          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
        2584         2816          391          174           57         1079 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1199          994          508          423         1973          102 
TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 
         925          494         1247          847          224            2 
TCGA-Y8-A898 TCGA-Y8-A8RZ 
         181          205 

  DEL PEAK 13(11Q24.2) MUTATED DEL PEAK 13(11Q24.2) WILD-TYPE 
                             4                              2 
  DEL PEAK 13(11Q24.2) MUTATED DEL PEAK 13(11Q24.2) WILD-TYPE 
                          3760                           5925 
  DEL PEAK 13(11Q24.2) MUTATED DEL PEAK 13(11Q24.2) WILD-TYPE 
                         223.0                          513.5 
[1] "4.0 - 3760.0 (223.0)" "2.0 - 5925.0 (513.5)"
[1] "hr=" "16" 
D20V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 13(11Q24.2) MUTATED         3        2        11        4
  DEL PEAK 13(11Q24.2) WILD-TYPE     119        9        31        8
D20V3, multiclass
           clus
vv          DEL PEAK 13(11Q24.2) MUTATED DEL PEAK 13(11Q24.2) WILD-TYPE
  STAGE I                              3                            119
  STAGE II                             2                              9
  STAGE III                           11                             31
  STAGE IV                             4                              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                              T1  T2 T3+T4
  DEL PEAK 13(11Q24.2) MUTATED     4   2    14
  DEL PEAK 13(11Q24.2) WILD-TYPE 126  16    36
D20V4, multiclass
       clus
vv      DEL PEAK 13(11Q24.2) MUTATED DEL PEAK 13(11Q24.2) WILD-TYPE
  T1                               4                            126
  T2                               2                             16
  T3+T4                           14                             36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 13(11Q24.2) MUTATED    3  6  2
  DEL PEAK 13(11Q24.2) WILD-TYPE 30 14  2
D20V5, multiclass
    clus
vv   DEL PEAK 13(11Q24.2) MUTATED DEL PEAK 13(11Q24.2) WILD-TYPE
  N0                            3                             30
  N1                            6                             14
  N2                            2                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK 13(11Q24.2) MUTATED    8  2  9
  DEL PEAK 13(11Q24.2) WILD-TYPE 73  6 87
D20V6, multiclass
    clus
vv   DEL PEAK 13(11Q24.2) MUTATED DEL PEAK 13(11Q24.2) WILD-TYPE
  M0                            8                             73
  M1                            2                              6
  MX                            9                             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                                cls
clus                               0   1
  DEL PEAK 13(11Q24.2) MUTATED     7  13
  DEL PEAK 13(11Q24.2) WILD-TYPE  51 127
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(11Q24.2) MUTATED      7   13
  DEL PEAK 13(11Q24.2) WILD-TYPE   51  127
        clus
vv       DEL PEAK 13(11Q24.2) MUTATED DEL PEAK 13(11Q24.2) WILD-TYPE
  FEMALE                            7                             51
  MALE                             13                            127
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(11Q24.2) MUTATED                                  0     1
  DEL PEAK 13(11Q24.2) WILD-TYPE                                2     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(11Q24.2) MUTATED                           4    13
  DEL PEAK 13(11Q24.2) WILD-TYPE                        45   116
D20V10, multiclass
                                  clus
vv                                 DEL PEAK 13(11Q24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      13
                                  clus
vv                                 DEL PEAK 13(11Q24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    45
  WHITE                                                       116
[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"
D20V11, binary
                                cls
clus                               0   1
  DEL PEAK 13(11Q24.2) MUTATED     0  14
  DEL PEAK 13(11Q24.2) WILD-TYPE   9 139
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(11Q24.2) MUTATED      0   14
  DEL PEAK 13(11Q24.2) WILD-TYPE    9  139
                        clus
vv                       DEL PEAK 13(11Q24.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           14
                        clus
vv                       DEL PEAK 13(11Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            139
[1] 2 2
[1] FALSE

Clustering(21) Variable = DEL PEAK 14(14Q11.2) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 14(14Q11.2) MUTATED    30   4
  DEL PEAK 14(14Q11.2) WILD-TYPE 136   3
  DEL PEAK 14(14Q11.2) MUTATED DEL PEAK 14(14Q11.2) WILD-TYPE 
                            34                            139 
  DEL PEAK 14(14Q11.2) MUTATED DEL PEAK 14(14Q11.2) WILD-TYPE 
                             4                              3 
$`DEL PEAK 14(14Q11.2) MUTATED`
TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-A5Y1 TCGA-AL-3473 
         554            3            2          140           87          763 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4103 
        1357           26          223          510          307          930 
TCGA-B9-4116 TCGA-B9-A5W8 TCGA-BQ-5876 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5894 
         627          207          586          921          403           84 
TCGA-DW-5560 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 
         353         2429         2460           97           10          208 
TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LD TCGA-GL-8500 TCGA-IA-A40U 
        1059          446          786         1967          841          511 
TCGA-IA-A40Y TCGA-MH-A854 TCGA-PJ-A5Z8 TCGA-SX-A71V 
          62           11          391          508 

$`DEL PEAK 14(14Q11.2) WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
          21          493          582           27            7           49 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
         780          729          709           23          597          600 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
         436          379          516            2          118            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-5398 
        1778         1636          412          923           67          595 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4104 
         659          747          108           14         1029         1049 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
         379           85         1536          857          803           14 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
          35          460         1338          671           64          585 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 
           5          102          167           52         2639          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 
        1938         1454         1242          792          792          771 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 
         233           29          364         3760         2948         2839 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
        1864         1533         1516          799          612          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         214          218          116          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        1240         1856         1670         1040          578          757 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 
           7           36         1575         1479         1194          765 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R 
         279         5925          393          112           32          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
         608          677          649          146            2            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         160          885          161         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         438          292          541          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
        2584         2816          174           57         1079         1199 
TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         994          423         1973          102          925          494 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 
        1247          847          224            2          186          181 
TCGA-Y8-A8RZ 
         205 

  DEL PEAK 14(14Q11.2) MUTATED DEL PEAK 14(14Q11.2) WILD-TYPE 
                             2                              2 
  DEL PEAK 14(14Q11.2) MUTATED DEL PEAK 14(14Q11.2) WILD-TYPE 
                          2460                           5925 
  DEL PEAK 14(14Q11.2) MUTATED DEL PEAK 14(14Q11.2) WILD-TYPE 
                         424.5                          541.0 
[1] "2.0 - 2460.0 (424.5)" "2.0 - 5925.0 (541.0)"
[1] "hr=" "6.4"
D21V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 14(14Q11.2) MUTATED        17        3        12        6
  DEL PEAK 14(14Q11.2) WILD-TYPE     105        8        30        6
D21V3, multiclass
           clus
vv          DEL PEAK 14(14Q11.2) MUTATED DEL PEAK 14(14Q11.2) WILD-TYPE
  STAGE I                             17                            105
  STAGE II                             3                              8
  STAGE III                           12                             30
  STAGE IV                             6                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2 T3+T4
  DEL PEAK 14(14Q11.2) MUTATED    18   4    18
  DEL PEAK 14(14Q11.2) WILD-TYPE 112  14    32
D21V4, multiclass
       clus
vv      DEL PEAK 14(14Q11.2) MUTATED DEL PEAK 14(14Q11.2) WILD-TYPE
  T1                              18                            112
  T2                               4                             14
  T3+T4                           18                             32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 14(14Q11.2) MUTATED    8  8  3
  DEL PEAK 14(14Q11.2) WILD-TYPE 25 12  1
D21V5, multiclass
    clus
vv   DEL PEAK 14(14Q11.2) MUTATED DEL PEAK 14(14Q11.2) WILD-TYPE
  N0                            8                             25
  N1                            8                             12
  N2                            3                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK 14(14Q11.2) MUTATED   17  3 18
  DEL PEAK 14(14Q11.2) WILD-TYPE 64  5 78
D21V6, multiclass
    clus
vv   DEL PEAK 14(14Q11.2) MUTATED DEL PEAK 14(14Q11.2) WILD-TYPE
  M0                           17                             64
  M1                            3                              5
  MX                           18                             78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                                cls
clus                               0   1
  DEL PEAK 14(14Q11.2) MUTATED    18  22
  DEL PEAK 14(14Q11.2) WILD-TYPE  40 118
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(14Q11.2) MUTATED     18   22
  DEL PEAK 14(14Q11.2) WILD-TYPE   40  118
        clus
vv       DEL PEAK 14(14Q11.2) MUTATED DEL PEAK 14(14Q11.2) WILD-TYPE
  FEMALE                           18                             40
  MALE                             22                            118
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(14Q11.2) MUTATED                                  0     1
  DEL PEAK 14(14Q11.2) WILD-TYPE                                2     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(14Q11.2) MUTATED                           8    28
  DEL PEAK 14(14Q11.2) WILD-TYPE                        41   101
D21V10, multiclass
                                  clus
vv                                 DEL PEAK 14(14Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      28
                                  clus
vv                                 DEL PEAK 14(14Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    41
  WHITE                                                       101
[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"
D21V11, binary
                                cls
clus                               0   1
  DEL PEAK 14(14Q11.2) MUTATED     1  33
  DEL PEAK 14(14Q11.2) WILD-TYPE   8 120
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(14Q11.2) MUTATED      1   33
  DEL PEAK 14(14Q11.2) WILD-TYPE    8  120
                        clus
vv                       DEL PEAK 14(14Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           33
                        clus
vv                       DEL PEAK 14(14Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            120
[1] 2 2
[1] FALSE

Clustering(22) Variable = DEL PEAK 15(15Q13.3) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 15(15Q13.3) MUTATED    15   4
  DEL PEAK 15(15Q13.3) WILD-TYPE 151   3
  DEL PEAK 15(15Q13.3) MUTATED DEL PEAK 15(15Q13.3) WILD-TYPE 
                            19                            154 
  DEL PEAK 15(15Q13.3) MUTATED DEL PEAK 15(15Q13.3) WILD-TYPE 
                             4                              3 
$`DEL PEAK 15(15Q13.3) MUTATED`
TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-A5Y1 TCGA-B1-5398 TCGA-B3-3926 TCGA-B9-A5W8 
         554            3           87          595          307          207 
TCGA-B9-A8YI TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6796 
          52           84           97           10          208         1059 
TCGA-G7-7502 TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7966 TCGA-IA-A40Y TCGA-PJ-A5Z8 
         786         1967         5925          112           62          391 
TCGA-Y8-A896 
         186 

$`DEL PEAK 15(15Q13.3) WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
          21          493          582           27            7           49 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
           2          140          780          729          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
         118            4         1778         1636          412          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M 
         763         1357           26           67          223          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 
         747          108          510           14         1029          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379           85         1536          857          803 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         627           14           35          460         1338          671 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-BQ-5875 
          64          585            5          102          167         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
         586          270         1938         1454         1242          792 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
         921          792          771          403          233           29 
TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
         364         3760         2948         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1516          799          612          232          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
         116          353          414         3950         1093         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          445           92         1240 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        2429         2460         1856         1670         1040          578 
TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
         757            7           36         1575         1479         1194 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
         765          446          279          393          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         167          511          608          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
           2            4          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 
         148         3035         2653         2584         2816          174 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
          57         1079         1199          994          508          423 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU 
        1973          102          925          494         1247          847 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         224            2          181          205 

  DEL PEAK 15(15Q13.3) MUTATED DEL PEAK 15(15Q13.3) WILD-TYPE 
                             3                              2 
  DEL PEAK 15(15Q13.3) MUTATED DEL PEAK 15(15Q13.3) WILD-TYPE 
                          5925                           3950 
  DEL PEAK 15(15Q13.3) MUTATED DEL PEAK 15(15Q13.3) WILD-TYPE 
                         207.0                          528.5 
[1] "3.0 - 5925.0 (207.0)" "2.0 - 3950.0 (528.5)"
[1] "hr=" "14" 
D22V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 15(15Q13.3) MUTATED         7        1        11        5
  DEL PEAK 15(15Q13.3) WILD-TYPE     115       10        31        7
D22V3, multiclass
           clus
vv          DEL PEAK 15(15Q13.3) MUTATED DEL PEAK 15(15Q13.3) WILD-TYPE
  STAGE I                              7                            115
  STAGE II                             1                             10
  STAGE III                           11                             31
  STAGE IV                             5                              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                              T1  T2 T3+T4
  DEL PEAK 15(15Q13.3) MUTATED     8   1    16
  DEL PEAK 15(15Q13.3) WILD-TYPE 122  17    34
D22V4, multiclass
       clus
vv      DEL PEAK 15(15Q13.3) MUTATED DEL PEAK 15(15Q13.3) WILD-TYPE
  T1                               8                            122
  T2                               1                             17
  T3+T4                           16                             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 15(15Q13.3) MUTATED    3 10  1
  DEL PEAK 15(15Q13.3) WILD-TYPE 30 10  3
D22V5, multiclass
    clus
vv   DEL PEAK 15(15Q13.3) MUTATED DEL PEAK 15(15Q13.3) WILD-TYPE
  N0                            3                             30
  N1                           10                             10
  N2                            1                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK 15(15Q13.3) MUTATED    9  3 12
  DEL PEAK 15(15Q13.3) WILD-TYPE 72  5 84
D22V6, multiclass
    clus
vv   DEL PEAK 15(15Q13.3) MUTATED DEL PEAK 15(15Q13.3) WILD-TYPE
  M0                            9                             72
  M1                            3                              5
  MX                           12                             84
[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"
D22V7, binary
                                cls
clus                               0   1
  DEL PEAK 15(15Q13.3) MUTATED    10  15
  DEL PEAK 15(15Q13.3) WILD-TYPE  48 125
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(15Q13.3) MUTATED     10   15
  DEL PEAK 15(15Q13.3) WILD-TYPE   48  125
        clus
vv       DEL PEAK 15(15Q13.3) MUTATED DEL PEAK 15(15Q13.3) WILD-TYPE
  FEMALE                           10                             48
  MALE                             15                            125
[1] 2 2
[1] FALSE
D22V8, continuous
D22V9, continuous
[1] "Remove cluster labels:"       "DEL PEAK 15(15Q13.3) MUTATED"
clus
  DEL PEAK 15(15Q13.3) MUTATED DEL PEAK 15(15Q13.3) WILD-TYPE 
                             2                             22 
                    TCGA-A4-A48D                     TCGA-B1-A654 
"DEL PEAK 15(15Q13.3) WILD-TYPE" "DEL PEAK 15(15Q13.3) WILD-TYPE" 
                    TCGA-B9-A44B                     TCGA-B9-A69E 
"DEL PEAK 15(15Q13.3) WILD-TYPE" "DEL PEAK 15(15Q13.3) WILD-TYPE" 
                    TCGA-GL-7773                     TCGA-GL-A59T 
"DEL PEAK 15(15Q13.3) WILD-TYPE" "DEL PEAK 15(15Q13.3) WILD-TYPE" 
                    TCGA-HE-A5NI                     TCGA-HE-A5NJ 
"DEL PEAK 15(15Q13.3) WILD-TYPE" "DEL PEAK 15(15Q13.3) WILD-TYPE" 
                    TCGA-IA-A40U                     TCGA-MH-A854 
"DEL PEAK 15(15Q13.3) WILD-TYPE" "DEL PEAK 15(15Q13.3) WILD-TYPE" 
                    TCGA-MH-A856                     TCGA-P4-A5E7 
"DEL PEAK 15(15Q13.3) WILD-TYPE" "DEL PEAK 15(15Q13.3) WILD-TYPE" 
                    TCGA-P4-A5EB                     TCGA-PJ-A5Z9 
"DEL PEAK 15(15Q13.3) WILD-TYPE" "DEL PEAK 15(15Q13.3) WILD-TYPE" 
                    TCGA-Q2-A5QZ                     TCGA-SX-A71S 
"DEL PEAK 15(15Q13.3) WILD-TYPE" "DEL PEAK 15(15Q13.3) WILD-TYPE" 
                    TCGA-SX-A71U                     TCGA-SX-A7SL 
"DEL PEAK 15(15Q13.3) WILD-TYPE" "DEL PEAK 15(15Q13.3) WILD-TYPE" 
                    TCGA-SX-A7SM                     TCGA-SX-A7SS 
"DEL PEAK 15(15Q13.3) WILD-TYPE" "DEL PEAK 15(15Q13.3) WILD-TYPE" 
                    TCGA-Y8-A894                     TCGA-Y8-A8RZ 
"DEL PEAK 15(15Q13.3) WILD-TYPE" "DEL PEAK 15(15Q13.3) WILD-TYPE" 
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(15Q13.3) MUTATED                                  0     1
  DEL PEAK 15(15Q13.3) WILD-TYPE                                2     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(15Q13.3) MUTATED                           4    17
  DEL PEAK 15(15Q13.3) WILD-TYPE                        45   112
D22V10, multiclass
                                  clus
vv                                 DEL PEAK 15(15Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      17
                                  clus
vv                                 DEL PEAK 15(15Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    45
  WHITE                                                       112
[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"
D22V11, binary
                                cls
clus                               0   1
  DEL PEAK 15(15Q13.3) MUTATED     1  20
  DEL PEAK 15(15Q13.3) WILD-TYPE   8 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(15Q13.3) MUTATED      1   20
  DEL PEAK 15(15Q13.3) WILD-TYPE    8  133
                        clus
vv                       DEL PEAK 15(15Q13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           20
                        clus
vv                       DEL PEAK 15(15Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            133
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK 16(16Q24.1) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 16(16Q24.1) MUTATED     3   2
  DEL PEAK 16(16Q24.1) WILD-TYPE 163   5
  DEL PEAK 16(16Q24.1) MUTATED DEL PEAK 16(16Q24.1) WILD-TYPE 
                             5                            168 
  DEL PEAK 16(16Q24.1) MUTATED DEL PEAK 16(16Q24.1) WILD-TYPE 
                             2                              5 
$`DEL PEAK 16(16Q24.1) MUTATED`
TCGA-A4-7287 TCGA-A4-A5Y1 TCGA-B9-A8YI TCGA-G7-A8LD TCGA-IA-A40X 
          21           87           52         1967          608 

$`DEL PEAK 16(16Q24.1) WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         554          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
           2          118            4         1778         1636          412 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         223          659          747          108          510           14 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379           85 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          857          803          627           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         460         1338          671           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
           5          102          167         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
         771          403          233           29          364           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         799          612          232          214          218          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         353          414         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
         419          114          445           92         1240         2429 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        2460         1856         1670         1040          578          757 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 
          97           10            7           36          208         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
        1479         1194         1059          765          446          786 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
         279         5925          393          112          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         178           91         2072          408          360         1726 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         167          511           62          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
           2            4          160          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         391          543          438          292           11          541 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         148         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         174           57         1079         1199          994          508 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS 
         423         1973          102          925          494         1247 
TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         847          224            2          186          181          205 

  DEL PEAK 16(16Q24.1) MUTATED DEL PEAK 16(16Q24.1) WILD-TYPE 
                            21                              2 
  DEL PEAK 16(16Q24.1) MUTATED DEL PEAK 16(16Q24.1) WILD-TYPE 
                          1967                           5925 
  DEL PEAK 16(16Q24.1) MUTATED DEL PEAK 16(16Q24.1) WILD-TYPE 
                            87                            509 
[1] "21.0 - 1967.0 (87.0)" "2.0 - 5925.0 (509.0)"
[1] "hr=" "18" 
D23V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 16(16Q24.1) MUTATED         3        0         4        2
  DEL PEAK 16(16Q24.1) WILD-TYPE     119       11        38       10
D23V3, multiclass
           clus
vv          DEL PEAK 16(16Q24.1) MUTATED DEL PEAK 16(16Q24.1) WILD-TYPE
  STAGE I                              3                            119
  STAGE II                             0                             11
  STAGE III                            4                             38
  STAGE IV                             2                             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                              T1  T2 T3+T4
  DEL PEAK 16(16Q24.1) MUTATED     4   0     5
  DEL PEAK 16(16Q24.1) WILD-TYPE 126  18    45
D23V4, multiclass
       clus
vv      DEL PEAK 16(16Q24.1) MUTATED DEL PEAK 16(16Q24.1) WILD-TYPE
  T1                               4                            126
  T2                               0                             18
  T3+T4                            5                             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 16(16Q24.1) MUTATED    1  3  1
  DEL PEAK 16(16Q24.1) WILD-TYPE 32 17  3
D23V5, multiclass
    clus
vv   DEL PEAK 16(16Q24.1) MUTATED DEL PEAK 16(16Q24.1) WILD-TYPE
  N0                            1                             32
  N1                            3                             17
  N2                            1                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK 16(16Q24.1) MUTATED    2  1  6
  DEL PEAK 16(16Q24.1) WILD-TYPE 79  7 90
D23V6, multiclass
    clus
vv   DEL PEAK 16(16Q24.1) MUTATED DEL PEAK 16(16Q24.1) WILD-TYPE
  M0                            2                             79
  M1                            1                              7
  MX                            6                             90
[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"
D23V7, binary
                                cls
clus                               0   1
  DEL PEAK 16(16Q24.1) MUTATED     4   5
  DEL PEAK 16(16Q24.1) WILD-TYPE  54 135
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(16Q24.1) MUTATED      4    5
  DEL PEAK 16(16Q24.1) WILD-TYPE   54  135
        clus
vv       DEL PEAK 16(16Q24.1) MUTATED DEL PEAK 16(16Q24.1) WILD-TYPE
  FEMALE                            4                             54
  MALE                              5                            135
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
[1] "Remove cluster labels:"       "DEL PEAK 16(16Q24.1) MUTATED"
clus
  DEL PEAK 16(16Q24.1) MUTATED DEL PEAK 16(16Q24.1) WILD-TYPE 
                             1                             23 
                    TCGA-A4-A48D                     TCGA-B1-A654 
"DEL PEAK 16(16Q24.1) WILD-TYPE" "DEL PEAK 16(16Q24.1) WILD-TYPE" 
                    TCGA-B9-A44B                     TCGA-B9-A69E 
"DEL PEAK 16(16Q24.1) WILD-TYPE" "DEL PEAK 16(16Q24.1) WILD-TYPE" 
                    TCGA-GL-7773                     TCGA-GL-A59T 
"DEL PEAK 16(16Q24.1) WILD-TYPE" "DEL PEAK 16(16Q24.1) WILD-TYPE" 
                    TCGA-HE-A5NI                     TCGA-HE-A5NJ 
"DEL PEAK 16(16Q24.1) WILD-TYPE" "DEL PEAK 16(16Q24.1) WILD-TYPE" 
                    TCGA-IA-A40U                     TCGA-MH-A854 
"DEL PEAK 16(16Q24.1) WILD-TYPE" "DEL PEAK 16(16Q24.1) WILD-TYPE" 
                    TCGA-MH-A856                     TCGA-P4-A5E7 
"DEL PEAK 16(16Q24.1) WILD-TYPE" "DEL PEAK 16(16Q24.1) WILD-TYPE" 
                    TCGA-P4-A5EB                     TCGA-PJ-A5Z9 
"DEL PEAK 16(16Q24.1) WILD-TYPE" "DEL PEAK 16(16Q24.1) WILD-TYPE" 
                    TCGA-Q2-A5QZ                     TCGA-SX-A71S 
"DEL PEAK 16(16Q24.1) WILD-TYPE" "DEL PEAK 16(16Q24.1) WILD-TYPE" 
                    TCGA-SX-A71U                     TCGA-SX-A7SL 
"DEL PEAK 16(16Q24.1) WILD-TYPE" "DEL PEAK 16(16Q24.1) WILD-TYPE" 
                    TCGA-SX-A7SM                     TCGA-SX-A7SS 
"DEL PEAK 16(16Q24.1) WILD-TYPE" "DEL PEAK 16(16Q24.1) WILD-TYPE" 
                    TCGA-Y8-A894                     TCGA-Y8-A896 
"DEL PEAK 16(16Q24.1) WILD-TYPE" "DEL PEAK 16(16Q24.1) WILD-TYPE" 
                    TCGA-Y8-A8RZ 
"DEL PEAK 16(16Q24.1) WILD-TYPE" 
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(16Q24.1) MUTATED                                  0     0
  DEL PEAK 16(16Q24.1) WILD-TYPE                                2     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(16Q24.1) MUTATED                           2     5
  DEL PEAK 16(16Q24.1) WILD-TYPE                        47   124
D23V10, multiclass
                                  clus
vv                                 DEL PEAK 16(16Q24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                       5
                                  clus
vv                                 DEL PEAK 16(16Q24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    47
  WHITE                                                       124
[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"
D23V11, binary
                                cls
clus                               0   1
  DEL PEAK 16(16Q24.1) MUTATED     0   7
  DEL PEAK 16(16Q24.1) WILD-TYPE   9 146
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(16Q24.1) MUTATED      0    7
  DEL PEAK 16(16Q24.1) WILD-TYPE    9  146
                        clus
vv                       DEL PEAK 16(16Q24.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            7
                        clus
vv                       DEL PEAK 16(16Q24.1) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            146
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK 17(19P13.3) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 17(19P13.3) MUTATED    13   3
  DEL PEAK 17(19P13.3) WILD-TYPE 153   4
  DEL PEAK 17(19P13.3) MUTATED DEL PEAK 17(19P13.3) WILD-TYPE 
                            16                            157 
  DEL PEAK 17(19P13.3) MUTATED DEL PEAK 17(19P13.3) WILD-TYPE 
                             3                              4 
$`DEL PEAK 17(19P13.3) MUTATED`
TCGA-A4-7286 TCGA-A4-8310 TCGA-A4-8517 TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B9-A44B 
         554          780          597           87          223           64 
TCGA-B9-A5W7 TCGA-BQ-5876 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-G7-6789 TCGA-G7-7502 
         585          586          233           29          208          786 
TCGA-G7-A8LD TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ 
        1967           62            4           57 

$`DEL PEAK 17(19P13.3) WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
          21          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
          49            2          140          729          709           23 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 
         600          436          379          516            2          118 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
           4         1778         1636          412          923          763 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
        1357           26           67          595          659          747 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         108          510           14         1029          307          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379           85         1536          857          803 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         627           14           35          460         1338          671 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
         207            5          102          167           52         2639 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         270         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
         792          771          403          364           84         3760 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        2948         2839         1864         1533         1516          799 
TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
         612          232          214          218          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         414         3950         1093         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         114          445           92         1240         2429         2460 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
        1856         1670         1040          578          757           97 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
          10            7           36         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
        1059          765          446          279         5925          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
         112          841           32          178           91         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         408          360         1726          167          511          608 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE 
         677          649          146            2          160          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          391          543          438          292 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
          11          541          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2816          391          174         1079         1199          994 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         508          423         1973          102          925          494 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 
        1247          847          224            2          186          181 
TCGA-Y8-A8RZ 
         205 

  DEL PEAK 17(19P13.3) MUTATED DEL PEAK 17(19P13.3) WILD-TYPE 
                             4                              2 
  DEL PEAK 17(19P13.3) MUTATED DEL PEAK 17(19P13.3) WILD-TYPE 
                          1967                           5925 
  DEL PEAK 17(19P13.3) MUTATED DEL PEAK 17(19P13.3) WILD-TYPE 
                           228                            510 
[1] "4.0 - 1967.0 (228.0)" "2.0 - 5925.0 (510.0)"
[1] "hr=" "14" 
D24V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 17(19P13.3) MUTATED         4        1         9        2
  DEL PEAK 17(19P13.3) WILD-TYPE     118       10        33       10
D24V3, multiclass
           clus
vv          DEL PEAK 17(19P13.3) MUTATED DEL PEAK 17(19P13.3) WILD-TYPE
  STAGE I                              4                            118
  STAGE II                             1                             10
  STAGE III                            9                             33
  STAGE IV                             2                             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                              T1  T2 T3+T4
  DEL PEAK 17(19P13.3) MUTATED     5   1    11
  DEL PEAK 17(19P13.3) WILD-TYPE 125  17    39
D24V4, multiclass
       clus
vv      DEL PEAK 17(19P13.3) MUTATED DEL PEAK 17(19P13.3) WILD-TYPE
  T1                               5                            125
  T2                               1                             17
  T3+T4                           11                             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 17(19P13.3) MUTATED    2  5  1
  DEL PEAK 17(19P13.3) WILD-TYPE 31 15  3
D24V5, multiclass
    clus
vv   DEL PEAK 17(19P13.3) MUTATED DEL PEAK 17(19P13.3) WILD-TYPE
  N0                            2                             31
  N1                            5                             15
  N2                            1                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK 17(19P13.3) MUTATED    4  1  9
  DEL PEAK 17(19P13.3) WILD-TYPE 77  7 87
D24V6, multiclass
    clus
vv   DEL PEAK 17(19P13.3) MUTATED DEL PEAK 17(19P13.3) WILD-TYPE
  M0                            4                             77
  M1                            1                              7
  MX                            9                             87
[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"
D24V7, binary
                                cls
clus                               0   1
  DEL PEAK 17(19P13.3) MUTATED     6  11
  DEL PEAK 17(19P13.3) WILD-TYPE  52 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(19P13.3) MUTATED      6   11
  DEL PEAK 17(19P13.3) WILD-TYPE   52  129
        clus
vv       DEL PEAK 17(19P13.3) MUTATED DEL PEAK 17(19P13.3) WILD-TYPE
  FEMALE                            6                             52
  MALE                             11                            129
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(19P13.3) MUTATED                                  0     1
  DEL PEAK 17(19P13.3) WILD-TYPE                                2     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(19P13.3) MUTATED                           4    12
  DEL PEAK 17(19P13.3) WILD-TYPE                        45   117
D24V10, multiclass
                                  clus
vv                                 DEL PEAK 17(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      12
                                  clus
vv                                 DEL PEAK 17(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    45
  WHITE                                                       117
[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"
D24V11, binary
                                cls
clus                               0   1
  DEL PEAK 17(19P13.3) MUTATED     0  16
  DEL PEAK 17(19P13.3) WILD-TYPE   9 137
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(19P13.3) MUTATED      0   16
  DEL PEAK 17(19P13.3) WILD-TYPE    9  137
                        clus
vv                       DEL PEAK 17(19P13.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           16
                        clus
vv                       DEL PEAK 17(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            137
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK 18(19Q13.42) MUTATION ANALYSIS
D25V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 18(19Q13.42) MUTATED    12   4
  DEL PEAK 18(19Q13.42) WILD-TYPE 154   3
  DEL PEAK 18(19Q13.42) MUTATED DEL PEAK 18(19Q13.42) WILD-TYPE 
                             16                             157 
  DEL PEAK 18(19Q13.42) MUTATED DEL PEAK 18(19Q13.42) WILD-TYPE 
                              4                               3 
$`DEL PEAK 18(19Q13.42) MUTATED`
TCGA-A4-7286 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8517 TCGA-A4-A5Y1 TCGA-B1-7332 
         554          140          780          597           87          223 
TCGA-BQ-5885 TCGA-BQ-5891 TCGA-BQ-7048 TCGA-BQ-7060 TCGA-F9-A4JJ TCGA-G7-6789 
         921           29         2839          214           97          208 
TCGA-G7-7502 TCGA-G7-A8LD TCGA-IA-A40Y TCGA-Q2-A5QZ 
         786         1967           62           57 

$`DEL PEAK 18(19Q13.42) WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
          21          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8518 
          49            2          729          709           23          600 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
         436          379          516            2          118            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
          26           67          595          659          747          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
         510           14         1029          307          930         1049 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
         379           85         1536          857          803          627 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
          14           35          460         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
         585          207            5          102          167           52 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
        2639          586          270         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5892 
         792          792          771          403          233          364 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
          84         3760         2948         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
         799          612          232          218          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         414         3950         1093         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         114          445           92         1240         2429         2460 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 
        1856         1670         1040          578          757           10 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
           7           36         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
         765          446          279         5925          393          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
         841           32          178           91         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 
         360         1726          167          511          608          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
         649          146            2            4          160          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          391          543          438          292 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
          11          541          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2816          391          174         1079         1199          994 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         508          423         1973          102          925          494 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 
        1247          847          224            2          186          181 
TCGA-Y8-A8RZ 
         205 

  DEL PEAK 18(19Q13.42) MUTATED DEL PEAK 18(19Q13.42) WILD-TYPE 
                             29                               2 
  DEL PEAK 18(19Q13.42) MUTATED DEL PEAK 18(19Q13.42) WILD-TYPE 
                           2839                            5925 
  DEL PEAK 18(19Q13.42) MUTATED DEL PEAK 18(19Q13.42) WILD-TYPE 
                          218.5                           510.0 
[1] "29.0 - 2839.0 (218.5)" "2.0 - 5925.0 (510.0)" 
[1] "hr=" "14" 
D25V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 18(19Q13.42) MUTATED         4        1         9        1
  DEL PEAK 18(19Q13.42) WILD-TYPE     118       10        33       11
D25V3, multiclass
           clus
vv          DEL PEAK 18(19Q13.42) MUTATED DEL PEAK 18(19Q13.42) WILD-TYPE
  STAGE I                               4                             118
  STAGE II                              1                              10
  STAGE III                             9                              33
  STAGE IV                              1                              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                               T1  T2 T3+T4
  DEL PEAK 18(19Q13.42) MUTATED     5   1    10
  DEL PEAK 18(19Q13.42) WILD-TYPE 125  17    40
D25V4, multiclass
       clus
vv      DEL PEAK 18(19Q13.42) MUTATED DEL PEAK 18(19Q13.42) WILD-TYPE
  T1                                5                             125
  T2                                1                              17
  T3+T4                            10                              40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2
  DEL PEAK 18(19Q13.42) MUTATED    3  3  1
  DEL PEAK 18(19Q13.42) WILD-TYPE 30 17  3
D25V5, multiclass
    clus
vv   DEL PEAK 18(19Q13.42) MUTATED DEL PEAK 18(19Q13.42) WILD-TYPE
  N0                             3                              30
  N1                             3                              17
  N2                             1                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1 MX
  DEL PEAK 18(19Q13.42) MUTATED    4  0 11
  DEL PEAK 18(19Q13.42) WILD-TYPE 77  8 85
D25V6, multiclass
    clus
vv   DEL PEAK 18(19Q13.42) MUTATED DEL PEAK 18(19Q13.42) WILD-TYPE
  M0                             4                              77
  M1                             0                               8
  MX                            11                              85
[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"
D25V7, binary
                                 cls
clus                                0   1
  DEL PEAK 18(19Q13.42) MUTATED     6  10
  DEL PEAK 18(19Q13.42) WILD-TYPE  52 130
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(19Q13.42) MUTATED      6   10
  DEL PEAK 18(19Q13.42) WILD-TYPE   52  130
        clus
vv       DEL PEAK 18(19Q13.42) MUTATED DEL PEAK 18(19Q13.42) WILD-TYPE
  FEMALE                             6                              52
  MALE                              10                             130
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
[1] "Remove cluster labels:"        "DEL PEAK 18(19Q13.42) MUTATED"
clus
  DEL PEAK 18(19Q13.42) MUTATED DEL PEAK 18(19Q13.42) WILD-TYPE 
                              2                              22 
                     TCGA-A4-A48D                      TCGA-B1-A654 
"DEL PEAK 18(19Q13.42) WILD-TYPE" "DEL PEAK 18(19Q13.42) WILD-TYPE" 
                     TCGA-B9-A44B                      TCGA-B9-A69E 
"DEL PEAK 18(19Q13.42) WILD-TYPE" "DEL PEAK 18(19Q13.42) WILD-TYPE" 
                     TCGA-GL-7773                      TCGA-GL-A59T 
"DEL PEAK 18(19Q13.42) WILD-TYPE" "DEL PEAK 18(19Q13.42) WILD-TYPE" 
                     TCGA-HE-A5NI                      TCGA-HE-A5NJ 
"DEL PEAK 18(19Q13.42) WILD-TYPE" "DEL PEAK 18(19Q13.42) WILD-TYPE" 
                     TCGA-IA-A40U                      TCGA-MH-A854 
"DEL PEAK 18(19Q13.42) WILD-TYPE" "DEL PEAK 18(19Q13.42) WILD-TYPE" 
                     TCGA-MH-A856                      TCGA-P4-A5E7 
"DEL PEAK 18(19Q13.42) WILD-TYPE" "DEL PEAK 18(19Q13.42) WILD-TYPE" 
                     TCGA-P4-A5EB                      TCGA-PJ-A5Z9 
"DEL PEAK 18(19Q13.42) WILD-TYPE" "DEL PEAK 18(19Q13.42) WILD-TYPE" 
                     TCGA-SX-A71S                      TCGA-SX-A71U 
"DEL PEAK 18(19Q13.42) WILD-TYPE" "DEL PEAK 18(19Q13.42) WILD-TYPE" 
                     TCGA-SX-A7SL                      TCGA-SX-A7SM 
"DEL PEAK 18(19Q13.42) WILD-TYPE" "DEL PEAK 18(19Q13.42) WILD-TYPE" 
                     TCGA-SX-A7SS                      TCGA-Y8-A894 
"DEL PEAK 18(19Q13.42) WILD-TYPE" "DEL PEAK 18(19Q13.42) WILD-TYPE" 
                     TCGA-Y8-A896                      TCGA-Y8-A8RZ 
"DEL PEAK 18(19Q13.42) WILD-TYPE" "DEL PEAK 18(19Q13.42) WILD-TYPE" 
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(19Q13.42) MUTATED                                  1     0
  DEL PEAK 18(19Q13.42) WILD-TYPE                                1     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(19Q13.42) MUTATED                           4    11
  DEL PEAK 18(19Q13.42) WILD-TYPE                        45   118
D25V10, multiclass
                                  clus
vv                                 DEL PEAK 18(19Q13.42) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       11
                                  clus
vv                                 DEL PEAK 18(19Q13.42) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     45
  WHITE                                                        118
[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"
D25V11, binary
                                 cls
clus                                0   1
  DEL PEAK 18(19Q13.42) MUTATED     0  15
  DEL PEAK 18(19Q13.42) WILD-TYPE   9 138
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(19Q13.42) MUTATED      0   15
  DEL PEAK 18(19Q13.42) WILD-TYPE    9  138
                        clus
vv                       DEL PEAK 18(19Q13.42) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            15
                        clus
vv                       DEL PEAK 18(19Q13.42) WILD-TYPE
  HISPANIC OR LATINO                                   9
  NOT HISPANIC OR LATINO                             138
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK 19(21Q22.3) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(21Q22.3) MUTATED    27   2
  DEL PEAK 19(21Q22.3) WILD-TYPE 139   5
  DEL PEAK 19(21Q22.3) MUTATED DEL PEAK 19(21Q22.3) WILD-TYPE 
                            29                            144 
  DEL PEAK 19(21Q22.3) MUTATED DEL PEAK 19(21Q22.3) WILD-TYPE 
                             2                              5 
$`DEL PEAK 19(21Q22.3) MUTATED`
TCGA-A4-7288 TCGA-A4-8516 TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-AL-3468 TCGA-B3-3925 
         493           23          516            2         1636         1029 
TCGA-B3-3926 TCGA-B9-4114 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-BQ-5875 
         307          857           64          585          207         2639 
TCGA-BQ-5885 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7061 TCGA-DZ-6134 TCGA-F9-A4JJ 
         921          233           84          218         1856           97 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6796 TCGA-GL-7966 TCGA-HE-A5NF TCGA-HE-A5NI 
          10          208         1059          112         2072          360 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GE TCGA-KV-A74V TCGA-PJ-A5Z9 
         511           62          885          161          174 

$`DEL PEAK 19(21Q22.3) WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         554           21            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         597          600          436          379          118           87 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
           4         1778          412          923          763         1357 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
          26           67          595          223          659          747 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
         108          510           14          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
          85         1536          803          627           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
         460         1338          671            5          102          167 
TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
          52          586          270         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 TCGA-BQ-5892 
         792          792          771          403           29          364 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 
         799          612          232          214          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         414         3950         1093         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         114          445           92         1240         2429         2460 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY 
        1670         1040          578          757            7           36 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
        1575         1479         1194          765          446          786 
TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
         279         1967         5925          393          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40X 
         178           91          408         1726          167          608 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
         677          649          146            2            4          160 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          391          543          438          292           11 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         541          148         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         391           57         1079         1199          994          508 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS 
         423         1973          102          925          494         1247 
TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         847          224            2          186          181          205 

  DEL PEAK 19(21Q22.3) MUTATED DEL PEAK 19(21Q22.3) WILD-TYPE 
                             2                              2 
  DEL PEAK 19(21Q22.3) MUTATED DEL PEAK 19(21Q22.3) WILD-TYPE 
                          2639                           5925 
  DEL PEAK 19(21Q22.3) MUTATED DEL PEAK 19(21Q22.3) WILD-TYPE 
                           307                            542 
[1] "2.0 - 2639.0 (307.0)" "2.0 - 5925.0 (542.0)"
[1] "hr=" "2.3"
D26V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 19(21Q22.3) MUTATED        13        3        11        4
  DEL PEAK 19(21Q22.3) WILD-TYPE     109        8        31        8
D26V3, multiclass
           clus
vv          DEL PEAK 19(21Q22.3) MUTATED DEL PEAK 19(21Q22.3) WILD-TYPE
  STAGE I                             13                            109
  STAGE II                             3                              8
  STAGE III                           11                             31
  STAGE IV                             4                              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                              T1  T2 T3+T4
  DEL PEAK 19(21Q22.3) MUTATED    14   5    14
  DEL PEAK 19(21Q22.3) WILD-TYPE 116  13    36
D26V4, multiclass
       clus
vv      DEL PEAK 19(21Q22.3) MUTATED DEL PEAK 19(21Q22.3) WILD-TYPE
  T1                              14                            116
  T2                               5                             13
  T3+T4                           14                             36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 19(21Q22.3) MUTATED    5  4  1
  DEL PEAK 19(21Q22.3) WILD-TYPE 28 16  3
D26V5, multiclass
    clus
vv   DEL PEAK 19(21Q22.3) MUTATED DEL PEAK 19(21Q22.3) WILD-TYPE
  N0                            5                             28
  N1                            4                             16
  N2                            1                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK 19(21Q22.3) MUTATED   12  3 14
  DEL PEAK 19(21Q22.3) WILD-TYPE 69  5 82
D26V6, multiclass
    clus
vv   DEL PEAK 19(21Q22.3) MUTATED DEL PEAK 19(21Q22.3) WILD-TYPE
  M0                           12                             69
  M1                            3                              5
  MX                           14                             82
[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"
D26V7, binary
                                cls
clus                               0   1
  DEL PEAK 19(21Q22.3) MUTATED    14  19
  DEL PEAK 19(21Q22.3) WILD-TYPE  44 121
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(21Q22.3) MUTATED     14   19
  DEL PEAK 19(21Q22.3) WILD-TYPE   44  121
        clus
vv       DEL PEAK 19(21Q22.3) MUTATED DEL PEAK 19(21Q22.3) WILD-TYPE
  FEMALE                           14                             44
  MALE                             19                            121
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(21Q22.3) MUTATED                                  0     1
  DEL PEAK 19(21Q22.3) WILD-TYPE                                2     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(21Q22.3) MUTATED                           5    23
  DEL PEAK 19(21Q22.3) WILD-TYPE                        44   106
D26V10, multiclass
                                  clus
vv                                 DEL PEAK 19(21Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      23
                                  clus
vv                                 DEL PEAK 19(21Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    44
  WHITE                                                       106
[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"
D26V11, binary
                                cls
clus                               0   1
  DEL PEAK 19(21Q22.3) MUTATED     1  25
  DEL PEAK 19(21Q22.3) WILD-TYPE   8 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(21Q22.3) MUTATED      1   25
  DEL PEAK 19(21Q22.3) WILD-TYPE    8  128
                        clus
vv                       DEL PEAK 19(21Q22.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           25
                        clus
vv                       DEL PEAK 19(21Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            128
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK 20(22Q12.2) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(22Q12.2) MUTATED    39   5
  DEL PEAK 20(22Q12.2) WILD-TYPE 127   2
  DEL PEAK 20(22Q12.2) MUTATED DEL PEAK 20(22Q12.2) WILD-TYPE 
                            44                            129 
  DEL PEAK 20(22Q12.2) MUTATED DEL PEAK 20(22Q12.2) WILD-TYPE 
                             5                              2 
$`DEL PEAK 20(22Q12.2) MUTATED`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-8098 TCGA-A4-8517 TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         554          493          140          597          118           87 
TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B9-A44B TCGA-B9-A5W8 
          26          223         1029          307           64          207 
TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5890 TCGA-BQ-5891 
        2639          270          792          921          233           29 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7055 TCGA-BQ-7056 
          84         3760         1864         1533          799          612 
TCGA-BQ-7061 TCGA-DZ-6131 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY 
         218         2429          578           97           10           36 
TCGA-G7-6789 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-7966 TCGA-IA-A40Y 
         208          765          446          786          112           62 
TCGA-J7-8537 TCGA-MH-A856 TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A7SL TCGA-SX-A7SM 
           4          541         2584           57          423         1973 
TCGA-Y8-A896 TCGA-Y8-A8RZ 
         186          205 

$`DEL PEAK 20(22Q12.2) WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
          21            3          582           27            7           49 
TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8518 
           2          780          729          709           23          600 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3467 
         436          379          516            2            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        1636          412          923          763         1357           67 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         595          659          747          108          510           14 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379           85         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
         671          585            5          102          167           52 
TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5886 TCGA-BQ-5887 
         586         1938         1454         1242          792          771 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7053 TCGA-BQ-7059 
         403          364         2948         2839         1516          232 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         214          116          353          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 
        1240         2460         1856         1670         1040          757 
TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-A4TM 
           7         1575         1479         1194         1059          279 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        1967         5925          393          841           32          178 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
          91         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         511          608          677          649          146            2 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         160          885          161         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         438          292           11          148         3035         2653 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2816          391          174         1079         1199          994 
TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU 
         508          102          925          494         1247          847 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A898 
         224            2          181 

  DEL PEAK 20(22Q12.2) MUTATED DEL PEAK 20(22Q12.2) WILD-TYPE 
                             4                              2 
  DEL PEAK 20(22Q12.2) MUTATED DEL PEAK 20(22Q12.2) WILD-TYPE 
                          3760                           5925 
  DEL PEAK 20(22Q12.2) MUTATED DEL PEAK 20(22Q12.2) WILD-TYPE 
                         288.5                          543.0 
[1] "4.0 - 3760.0 (288.5)" "2.0 - 5925.0 (543.0)"
[1] "hr=" "7.1"
D27V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 20(22Q12.2) MUTATED        16        3        22        7
  DEL PEAK 20(22Q12.2) WILD-TYPE     106        8        20        5
D27V3, multiclass
           clus
vv          DEL PEAK 20(22Q12.2) MUTATED DEL PEAK 20(22Q12.2) WILD-TYPE
  STAGE I                             16                            106
  STAGE II                             3                              8
  STAGE III                           22                             20
  STAGE IV                             7                              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                              T1  T2 T3+T4
  DEL PEAK 20(22Q12.2) MUTATED    18   5    27
  DEL PEAK 20(22Q12.2) WILD-TYPE 112  13    23
D27V4, multiclass
       clus
vv      DEL PEAK 20(22Q12.2) MUTATED DEL PEAK 20(22Q12.2) WILD-TYPE
  T1                              18                            112
  T2                               5                             13
  T3+T4                           27                             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"
                                vv
clus                             N0 N1 N2
  DEL PEAK 20(22Q12.2) MUTATED    8 13  2
  DEL PEAK 20(22Q12.2) WILD-TYPE 25  7  2
D27V5, multiclass
    clus
vv   DEL PEAK 20(22Q12.2) MUTATED DEL PEAK 20(22Q12.2) WILD-TYPE
  N0                            8                             25
  N1                           13                              7
  N2                            2                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK 20(22Q12.2) MUTATED   22  5 21
  DEL PEAK 20(22Q12.2) WILD-TYPE 59  3 75
D27V6, multiclass
    clus
vv   DEL PEAK 20(22Q12.2) MUTATED DEL PEAK 20(22Q12.2) WILD-TYPE
  M0                           22                             59
  M1                            5                              3
  MX                           21                             75
[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"
D27V7, binary
                                cls
clus                               0   1
  DEL PEAK 20(22Q12.2) MUTATED    23  27
  DEL PEAK 20(22Q12.2) WILD-TYPE  35 113
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(22Q12.2) MUTATED     23   27
  DEL PEAK 20(22Q12.2) WILD-TYPE   35  113
        clus
vv       DEL PEAK 20(22Q12.2) MUTATED DEL PEAK 20(22Q12.2) WILD-TYPE
  FEMALE                           23                             35
  MALE                             27                            113
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(22Q12.2) MUTATED                                  0     3
  DEL PEAK 20(22Q12.2) WILD-TYPE                                2     1
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(22Q12.2) MUTATED                          10    34
  DEL PEAK 20(22Q12.2) WILD-TYPE                        39    95
D27V10, multiclass
                                  clus
vv                                 DEL PEAK 20(22Q12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      34
                                  clus
vv                                 DEL PEAK 20(22Q12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         1
  BLACK OR AFRICAN AMERICAN                                    39
  WHITE                                                        95
[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"
D27V11, binary
                                cls
clus                               0   1
  DEL PEAK 20(22Q12.2) MUTATED     3  34
  DEL PEAK 20(22Q12.2) WILD-TYPE   6 119
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(22Q12.2) MUTATED      3   34
  DEL PEAK 20(22Q12.2) WILD-TYPE    6  119
                        clus
vv                       DEL PEAK 20(22Q12.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           34
                        clus
vv                       DEL PEAK 20(22Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            119
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK 21(XP11.22) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(XP11.22) MUTATED    12   4
  DEL PEAK 21(XP11.22) WILD-TYPE 154   3
  DEL PEAK 21(XP11.22) MUTATED DEL PEAK 21(XP11.22) WILD-TYPE 
                            16                            157 
  DEL PEAK 21(XP11.22) MUTATED DEL PEAK 21(XP11.22) WILD-TYPE 
                             4                              3 
$`DEL PEAK 21(XP11.22) MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4116 
         554           21           87          223          307          627 
TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5877 TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 
          64          586          270         2429           97           10 
TCGA-G7-7501 TCGA-G7-A8LD TCGA-J7-8537 TCGA-Q2-A5QZ 
         446         1967            4           57 

$`DEL PEAK 21(XP11.22) WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
         493            3          582           27            7           49 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
           2          140          780          729          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ 
         597          600          436          379          516            2 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
         118            4         1778         1636          412          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         763         1357           26           67          595          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 
         747          108          510           14         1029          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379           85         1536          857          803 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 
          14           35          460         1338          671          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
         207            5          102          167           52         2639 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
         771          403          233           29          364           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         799          612          232          214          218          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         353          414         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 
         419          114          445           92         1240         2460 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF 
        1856         1670         1040          578          757            7 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
          36          208         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
         765          786          279         5925          393          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
         841           32          178           91         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
         360         1726          167          511          608           62 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE 
         677          649          146            2          160          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          391          543          438          292 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
          11          541          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2816          391          174         1079         1199          994 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         508          423         1973          102          925          494 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 
        1247          847          224            2          186          181 
TCGA-Y8-A8RZ 
         205 

  DEL PEAK 21(XP11.22) MUTATED DEL PEAK 21(XP11.22) WILD-TYPE 
                             4                              2 
  DEL PEAK 21(XP11.22) MUTATED DEL PEAK 21(XP11.22) WILD-TYPE 
                          2429                           5925 
  DEL PEAK 21(XP11.22) MUTATED DEL PEAK 21(XP11.22) WILD-TYPE 
                         246.5                          516.0 
[1] "4.0 - 2429.0 (246.5)" "2.0 - 5925.0 (516.0)"
[1] "hr=" "15" 
D28V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 21(XP11.22) MUTATED         4        1        11        2
  DEL PEAK 21(XP11.22) WILD-TYPE     118       10        31       10
D28V3, multiclass
           clus
vv          DEL PEAK 21(XP11.22) MUTATED DEL PEAK 21(XP11.22) WILD-TYPE
  STAGE I                              4                            118
  STAGE II                             1                             10
  STAGE III                           11                             31
  STAGE IV                             2                             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                              T1  T2 T3+T4
  DEL PEAK 21(XP11.22) MUTATED     5   2    13
  DEL PEAK 21(XP11.22) WILD-TYPE 125  16    37
D28V4, multiclass
       clus
vv      DEL PEAK 21(XP11.22) MUTATED DEL PEAK 21(XP11.22) WILD-TYPE
  T1                               5                            125
  T2                               2                             16
  T3+T4                           13                             37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 21(XP11.22) MUTATED    2  6  1
  DEL PEAK 21(XP11.22) WILD-TYPE 31 14  3
D28V5, multiclass
    clus
vv   DEL PEAK 21(XP11.22) MUTATED DEL PEAK 21(XP11.22) WILD-TYPE
  N0                            2                             31
  N1                            6                             14
  N2                            1                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK 21(XP11.22) MUTATED    7  1  9
  DEL PEAK 21(XP11.22) WILD-TYPE 74  7 87
D28V6, multiclass
    clus
vv   DEL PEAK 21(XP11.22) MUTATED DEL PEAK 21(XP11.22) WILD-TYPE
  M0                            7                             74
  M1                            1                              7
  MX                            9                             87
[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"
D28V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(XP11.22) MUTATED    12   8
  DEL PEAK 21(XP11.22) WILD-TYPE  46 132
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(XP11.22) MUTATED     12    8
  DEL PEAK 21(XP11.22) WILD-TYPE   46  132
        clus
vv       DEL PEAK 21(XP11.22) MUTATED DEL PEAK 21(XP11.22) WILD-TYPE
  FEMALE                           12                             46
  MALE                              8                            132
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(XP11.22) MUTATED                                  0     2
  DEL PEAK 21(XP11.22) WILD-TYPE                                2     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(XP11.22) MUTATED                           7     9
  DEL PEAK 21(XP11.22) WILD-TYPE                        42   120
D28V10, multiclass
                                  clus
vv                                 DEL PEAK 21(XP11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                       9
                                  clus
vv                                 DEL PEAK 21(XP11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    42
  WHITE                                                       120
[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"
D28V11, binary
                                cls
clus                               0   1
  DEL PEAK 21(XP11.22) MUTATED     0  13
  DEL PEAK 21(XP11.22) WILD-TYPE   9 140
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(XP11.22) MUTATED      0   13
  DEL PEAK 21(XP11.22) WILD-TYPE    9  140
                        clus
vv                       DEL PEAK 21(XP11.22) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           13
                        clus
vv                       DEL PEAK 21(XP11.22) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            140
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK 22(XQ28) MUTATION ANALYSIS
D29V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 22(XQ28) MUTATED    11   3
  DEL PEAK 22(XQ28) WILD-TYPE 155   4
  DEL PEAK 22(XQ28) MUTATED DEL PEAK 22(XQ28) WILD-TYPE 
                         14                         159 
  DEL PEAK 22(XQ28) MUTATED DEL PEAK 22(XQ28) WILD-TYPE 
                          3                           4 
$`DEL PEAK 22(XQ28) MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B3-3926 
         554           21            3           87          223          307 
TCGA-BQ-5876 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A8LD 
         586           97           10          765          446         1967 
TCGA-J7-8537 TCGA-Q2-A5QZ 
           4           57 

$`DEL PEAK 22(XQ28) WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
         493          582           27            7           49            2 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
         140          780          729          709           23          597 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 
         600          436          379          516            2          118 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
           4         1778         1636          412          923          763 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
        1357           26           67          595          659          747 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
         108          510           14         1029          930         1049 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
         379           85         1536          857          803          627 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
          14           35          460         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
         585          207            5          102          167           52 
TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
        2639          270         1938         1454         1242          792 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
         921          792          771          403          233           29 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
         364           84         3760         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
        1533         1516          799          612          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         218          116          353          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1240         2429         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 
         578          757            7           36          208         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
        1479         1194         1059          786          279         5925 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
         393          112          841           32          178           91 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
        2072          408          360         1726          167          511 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         608           62          677          649          146            2 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         160          885          161         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
         438          292           11          541          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R 
        2653         2584         2816          391          174         1079 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1199          994          508          423         1973          102 
TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 
         925          494         1247          847          224            2 
TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
         186          181          205 

  DEL PEAK 22(XQ28) MUTATED DEL PEAK 22(XQ28) WILD-TYPE 
                          3                           2 
  DEL PEAK 22(XQ28) MUTATED DEL PEAK 22(XQ28) WILD-TYPE 
                       1967                        5925 
  DEL PEAK 22(XQ28) MUTATED DEL PEAK 22(XQ28) WILD-TYPE 
                        160                         516 
[1] "3.0 - 1967.0 (160.0)" "2.0 - 5925.0 (516.0)"
[1] "hr=" "17" 
D29V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 22(XQ28) MUTATED         5        1        10        2
  DEL PEAK 22(XQ28) WILD-TYPE     117       10        32       10
D29V3, multiclass
           clus
vv          DEL PEAK 22(XQ28) MUTATED DEL PEAK 22(XQ28) WILD-TYPE
  STAGE I                           5                         117
  STAGE II                          1                          10
  STAGE III                        10                          32
  STAGE IV                          2                          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                           T1  T2 T3+T4
  DEL PEAK 22(XQ28) MUTATED     7   1    11
  DEL PEAK 22(XQ28) WILD-TYPE 123  17    39
D29V4, multiclass
       clus
vv      DEL PEAK 22(XQ28) MUTATED DEL PEAK 22(XQ28) WILD-TYPE
  T1                            7                         123
  T2                            1                          17
  T3+T4                        11                          39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2
  DEL PEAK 22(XQ28) MUTATED    2  6  1
  DEL PEAK 22(XQ28) WILD-TYPE 31 14  3
D29V5, multiclass
    clus
vv   DEL PEAK 22(XQ28) MUTATED DEL PEAK 22(XQ28) WILD-TYPE
  N0                         2                          31
  N1                         6                          14
  N2                         1                           3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          M0 M1 MX
  DEL PEAK 22(XQ28) MUTATED    8  1  9
  DEL PEAK 22(XQ28) WILD-TYPE 73  7 87
D29V6, multiclass
    clus
vv   DEL PEAK 22(XQ28) MUTATED DEL PEAK 22(XQ28) WILD-TYPE
  M0                         8                          73
  M1                         1                           7
  MX                         9                          87
[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"
D29V7, binary
                             cls
clus                            0   1
  DEL PEAK 22(XQ28) MUTATED    11   8
  DEL PEAK 22(XQ28) WILD-TYPE  47 132
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(XQ28) MUTATED     11    8
  DEL PEAK 22(XQ28) WILD-TYPE   47  132
        clus
vv       DEL PEAK 22(XQ28) MUTATED DEL PEAK 22(XQ28) WILD-TYPE
  FEMALE                        11                          47
  MALE                           8                         132
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, continuous
[1] "Remove cluster labels:"    "DEL PEAK 22(XQ28) MUTATED"
clus
  DEL PEAK 22(XQ28) MUTATED DEL PEAK 22(XQ28) WILD-TYPE 
                          2                          22 
                 TCGA-A4-A48D                  TCGA-B1-A654 
"DEL PEAK 22(XQ28) WILD-TYPE" "DEL PEAK 22(XQ28) WILD-TYPE" 
                 TCGA-B9-A44B                  TCGA-B9-A69E 
"DEL PEAK 22(XQ28) WILD-TYPE" "DEL PEAK 22(XQ28) WILD-TYPE" 
                 TCGA-GL-7773                  TCGA-GL-A59T 
"DEL PEAK 22(XQ28) WILD-TYPE" "DEL PEAK 22(XQ28) WILD-TYPE" 
                 TCGA-HE-A5NI                  TCGA-HE-A5NJ 
"DEL PEAK 22(XQ28) WILD-TYPE" "DEL PEAK 22(XQ28) WILD-TYPE" 
                 TCGA-IA-A40U                  TCGA-MH-A854 
"DEL PEAK 22(XQ28) WILD-TYPE" "DEL PEAK 22(XQ28) WILD-TYPE" 
                 TCGA-MH-A856                  TCGA-P4-A5E7 
"DEL PEAK 22(XQ28) WILD-TYPE" "DEL PEAK 22(XQ28) WILD-TYPE" 
                 TCGA-P4-A5EB                  TCGA-PJ-A5Z9 
"DEL PEAK 22(XQ28) WILD-TYPE" "DEL PEAK 22(XQ28) WILD-TYPE" 
                 TCGA-SX-A71S                  TCGA-SX-A71U 
"DEL PEAK 22(XQ28) WILD-TYPE" "DEL PEAK 22(XQ28) WILD-TYPE" 
                 TCGA-SX-A7SL                  TCGA-SX-A7SM 
"DEL PEAK 22(XQ28) WILD-TYPE" "DEL PEAK 22(XQ28) WILD-TYPE" 
                 TCGA-SX-A7SS                  TCGA-Y8-A894 
"DEL PEAK 22(XQ28) WILD-TYPE" "DEL PEAK 22(XQ28) WILD-TYPE" 
                 TCGA-Y8-A896                  TCGA-Y8-A8RZ 
"DEL PEAK 22(XQ28) WILD-TYPE" "DEL PEAK 22(XQ28) WILD-TYPE" 
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(XQ28) MUTATED                                  0     2
  DEL PEAK 22(XQ28) WILD-TYPE                                2     2
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(XQ28) MUTATED                           5    10
  DEL PEAK 22(XQ28) WILD-TYPE                        44   119
D29V10, multiclass
                                  clus
vv                                 DEL PEAK 22(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    2
  BLACK OR AFRICAN AMERICAN                                5
  WHITE                                                   10
                                  clus
vv                                 DEL PEAK 22(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 44
  WHITE                                                    119
[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"
D29V11, binary
                             cls
clus                            0   1
  DEL PEAK 22(XQ28) MUTATED     0  14
  DEL PEAK 22(XQ28) WILD-TYPE   9 139
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(XQ28) MUTATED      0   14
  DEL PEAK 22(XQ28) WILD-TYPE    9  139
                        clus
vv                       DEL PEAK 22(XQ28) MUTATED DEL PEAK 22(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             0                           9
  NOT HISPANIC OR LATINO                        14                         139
[1] 2 2
[1] FALSE
