[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"       "-oTACC-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/ACC-TP/10005775/ACC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ACC-TP/10013670/transformed.cor.cli.txt"

nPatients in clinical file=82, in cluster file=90, common to both=80
[1] 45 80
[1] "AMP PEAK  1(1Q22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         15                          65 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         15                          65 
[1] "AMP PEAK  2(4P16.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                           36                            44 
  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                           36                            44 
[1] "AMP PEAK  3(4Q35.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                           26                            54 
  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                           26                            54 
[1] "AMP PEAK  4(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            59                             21 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            59                             21 
[1] "AMP PEAK  5(5Q35.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                           57                            23 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                           57                            23 
[1] "AMP PEAK  6(6P21.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(6P21.31) WILD-TYPE 
                            14                             66 
  AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(6P21.31) WILD-TYPE 
                            14                             66 
[1] "AMP PEAK  7(6Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(6Q24.3) WILD-TYPE 
                           15                            65 
  AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(6Q24.3) WILD-TYPE 
                           15                            65 
[1] "AMP PEAK  8(7P22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                           48                            32 
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                           48                            32 
[1] "AMP PEAK  9(9Q31.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(9Q31.3) WILD-TYPE 
                           27                            53 
  AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(9Q31.3) WILD-TYPE 
                           27                            53 
[1] "AMP PEAK 10(12Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                            62                             18 
  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                            62                             18 
[1] "AMP PEAK 11(14Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                            23                             57 
  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                            23                             57 
[1] "AMP PEAK 12(16P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                            45                             35 
  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                            45                             35 
[1] "AMP PEAK 13(16Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                            50                             30 
  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                            50                             30 
[1] "AMP PEAK 14(16Q24.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                            44                             36 
  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                            44                             36 
[1] "AMP PEAK 15(17Q25.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(17Q25.3) WILD-TYPE 
                            14                             66 
  AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(17Q25.3) WILD-TYPE 
                            14                             66 
[1] "AMP PEAK 16(19P13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                             51                              29 
  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                             51                              29 
[1] "AMP PEAK 17(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                          48                           32 
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                          48                           32 
[1] "AMP PEAK 18(XP11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(XP11.22) WILD-TYPE 
                            42                             38 
  AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(XP11.22) WILD-TYPE 
                            42                             38 
[1] "AMP PEAK 19(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE 
                         40                          40 
  AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE 
                         40                          40 
[1] "DEL PEAK  1(1P36.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            35                             45 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            35                             45 
[1] "DEL PEAK  2(1Q43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                         17                          63 
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                         17                          63 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           17                            63 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           17                            63 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           20                            60 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           20                            60 
[1] "DEL PEAK  5(3Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                            21                             59 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                            21                             59 
[1] "DEL PEAK  6(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           19                            61 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           19                            61 
[1] "DEL PEAK  7(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                           23                            57 
  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                           23                            57 
[1] "DEL PEAK  8(6P24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE 
                           18                            62 
  DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE 
                           18                            62 
[1] "DEL PEAK  9(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                         20                          60 
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                         20                          60 
[1] "DEL PEAK 10(7Q32.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(7Q32.3) MUTATED DEL PEAK 10(7Q32.3) WILD-TYPE 
                            8                            72 
  DEL PEAK 10(7Q32.3) MUTATED DEL PEAK 10(7Q32.3) WILD-TYPE 
                            8                            72 
[1] "DEL PEAK 11(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE 
                         21                          59 
  DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE 
                         21                          59 
[1] "DEL PEAK 12(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           24                            56 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           24                            56 
[1] "DEL PEAK 13(10Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE 
                             9                             71 
  DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE 
                             9                             71 
[1] "DEL PEAK 14(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                            26                             54 
  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                            26                             54 
[1] "DEL PEAK 15(11Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                            23                             57 
  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                            23                             57 
[1] "DEL PEAK 16(12Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE 
                             5                             75 
  DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE 
                             5                             75 
[1] "DEL PEAK 17(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                            36                             44 
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                            36                             44 
[1] "DEL PEAK 18(14Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE 
                            18                             62 
  DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE 
                            18                             62 
[1] "DEL PEAK 19(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                             6                             74 
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                             6                             74 
[1] "DEL PEAK 20(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(16Q23.1) MUTATED DEL PEAK 20(16Q23.1) WILD-TYPE 
                             6                             74 
  DEL PEAK 20(16Q23.1) MUTATED DEL PEAK 20(16Q23.1) WILD-TYPE 
                             6                             74 
[1] "DEL PEAK 21(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(17Q11.2) MUTATED DEL PEAK 21(17Q11.2) WILD-TYPE 
                            23                             57 
  DEL PEAK 21(17Q11.2) MUTATED DEL PEAK 21(17Q11.2) WILD-TYPE 
                            23                             57 
[1] "DEL PEAK 22(17Q21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(17Q21.31) MUTATED DEL PEAK 22(17Q21.31) WILD-TYPE 
                             26                              54 
  DEL PEAK 22(17Q21.31) MUTATED DEL PEAK 22(17Q21.31) WILD-TYPE 
                             26                              54 
[1] "DEL PEAK 23(17Q24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(17Q24.2) MUTATED DEL PEAK 23(17Q24.2) WILD-TYPE 
                            24                             56 
  DEL PEAK 23(17Q24.2) MUTATED DEL PEAK 23(17Q24.2) WILD-TYPE 
                            24                             56 
[1] "DEL PEAK 24(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(18Q21.2) MUTATED DEL PEAK 24(18Q21.2) WILD-TYPE 
                            34                             46 
  DEL PEAK 24(18Q21.2) MUTATED DEL PEAK 24(18Q21.2) WILD-TYPE 
                            34                             46 
[1] "DEL PEAK 25(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                             9                             71 
  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                             9                             71 
[1] "DEL PEAK 26(22Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE 
                            46                             34 
  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE 
                            46                             34 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "NEOPLASM.DISEASESTAGE"                 
 [6] "PATHOLOGY.T.STAGE"                     
 [7] "PATHOLOGY.N.STAGE"                     
 [8] "PATHOLOGY.M.STAGE"                     
 [9] "DCCUPLOADDATE"                         
[10] "GENDER"                                
[11] "RADIATIONTHERAPY"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCHNUMBER"                           

Input Data has 15 rows and 80 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
          NA           NA         1942           NA           NA         2428 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
          NA           NA         1183           NA           NA           NA 
TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
        2782           NA         1259           NA         1227         1424 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
         309         1255          670           NA          889          149 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
         674         3688          383          488           NA         1541 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
        1924          950           NA          211         1029         2723 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
          NA         2842          528          253         1130           NA 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
        1414         2673         4673         3659         1525         1091 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
          NA           NA         3897          724          840          628 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
         555          645          487           NA           NA           NA 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
          NA           NA         1589           NA           NA         2222 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
          NA         1858         1916         1949         1583          639 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-P6-A5OH TCGA-PK-A5H9 
         882          365          709           NA           NA          307 
TCGA-PK-A5HA TCGA-PK-A5HB 
         830         1293 
Variable 1:'AGE':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "GENDER"                "ETHNICITY"            
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 80 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=46, 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 
 8 39 11 18 
[1] "table(vv)"
vv
T1 T2 T3 T4 
 8 39 11 18 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 8 39 11 18 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
 8 39 11 18 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1Q22) MUTATION ANALYSIS
D1V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  1(1Q22) MUTATED    5 10
  AMP PEAK  1(1Q22) WILD-TYPE 47 17
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         15                          64 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         10                          17 
$`AMP PEAK  1(1Q22) MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JK 
       44.55        55.13        16.11        18.12        69.21        41.26 
TCGA-OR-A5JV TCGA-OR-A5K0 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KX TCGA-OR-A5LC 
       50.66        33.83         8.32        11.31        35.87         5.23 
TCGA-OR-A5LE TCGA-OR-A5LL TCGA-P6-A5OG 
       21.76        53.03        12.59 

$`AMP PEAK  1(1Q22) WILD-TYPE`
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 
       63.85        15.45        12.00        79.82        19.04        38.89 
TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH 
       30.31        57.53        91.46        41.39        17.79        40.34 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       46.82        10.16        22.03        18.48        29.23         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW 
       22.16       121.25        12.59        16.04         9.50        63.25 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       31.23        18.15         6.94        89.52        32.68        93.44 
TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       17.36        37.15        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        12.85         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD 
       20.65        18.25        21.21        16.01        39.58        39.35 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM 
       14.63        52.24        78.41        36.33        73.05        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       62.99        64.08        52.04        21.01        29.00        12.00 
TCGA-OU-A5PI TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       23.31        10.09        27.29        42.51 

  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                       5.23                        4.11 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                      69.21                      153.63 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                      33.83                       30.77 
[1] "5.2 - 69.2 (33.8)"  "4.1 - 153.6 (30.8)"
[1] "hr=" "3.2"
D1V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  1(1Q22) MUTATED         1        6         3        5
  AMP PEAK  1(1Q22) WILD-TYPE       7       28        14       12
D1V3, multiclass
           clus
vv          AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  STAGE I                           1                           7
  STAGE II                          6                          28
  STAGE III                         3                          14
  STAGE IV                          5                          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  1(1Q22) MUTATED    1  7  3  4
  AMP PEAK  1(1Q22) WILD-TYPE  7 32  8 14
D1V4, multiclass
    clus
vv   AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  T1                         1                           7
  T2                         7                          32
  T3                         3                           8
  T4                         4                          14
[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"
D1V5, binary
                             cls
clus                           0  1
  AMP PEAK  1(1Q22) MUTATED   14  1
  AMP PEAK  1(1Q22) WILD-TYPE 53  9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q22) MUTATED     14    1
  AMP PEAK  1(1Q22) WILD-TYPE   53    9
   clus
vv  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  0                        14                          53
  1                         1                           9
[1] 2 2
[1] FALSE
D1V6, binary
                             cls
clus                           0  1
  AMP PEAK  1(1Q22) MUTATED   10  5
  AMP PEAK  1(1Q22) WILD-TYPE 42 23
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q22) MUTATED     10    5
  AMP PEAK  1(1Q22) WILD-TYPE   42   23
        clus
vv       AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  FEMALE                        10                          42
  MALE                           5                          23
[1] 2 2
[1] FALSE
D1V7, binary
                             cls
clus                           0  1
  AMP PEAK  1(1Q22) MUTATED    2  4
  AMP PEAK  1(1Q22) WILD-TYPE  6 23
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q22) MUTATED      2    4
  AMP PEAK  1(1Q22) WILD-TYPE    6   23
                        clus
vv                       AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  HISPANIC OR LATINO                             2                           6
  NOT HISPANIC OR LATINO                         4                          23
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(4P16.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(4P16.3) MUTATED   26 10
  AMP PEAK  2(4P16.3) WILD-TYPE 26 17
  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                           36                            43 
  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                           10                            17 
$`AMP PEAK  2(4P16.3) MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA 
       44.55        15.45        12.00        16.11        38.89        30.31 
TCGA-OR-A5JC TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       57.53        41.39        40.34        46.82        10.16        41.26 
TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       22.03         4.90        22.16       121.25        16.04        50.66 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       93.44        17.36         8.32        46.49        87.88       153.63 
TCGA-OR-A5KW TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LK 
       50.14        16.01        39.58        14.63        78.41        73.05 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       53.03        61.08        62.99        29.00        12.00        23.31 

$`AMP PEAK  2(4P16.3) WILD-TYPE`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD 
       55.13        63.85        79.82        19.04        18.12        91.46 
TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JU 
       69.21        17.79        18.48        29.23        12.59         9.50 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       63.25        31.23        18.15         6.94        33.83        89.52 
TCGA-OR-A5K2 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KY 
       32.68        37.15        11.31       120.30        35.87        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
        4.11       128.12        23.80        27.62        20.65        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LJ 
       21.21         5.23        39.35        21.76        52.24        36.33 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       64.08        52.04        21.01        12.59        10.09        27.29 
TCGA-PK-A5HB 
       42.51 

  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                         4.90                          4.11 
  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                       153.63                        128.12 
  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                        39.96                         27.62 
[1] "4.9 - 153.6 (40.0)" "4.1 - 128.1 (27.6)"
[1] "hr=" "1.6"
D2V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  2(4P16.3) MUTATED         4       17         7        7
  AMP PEAK  2(4P16.3) WILD-TYPE       4       17        10       10
D2V3, multiclass
           clus
vv          AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE
  STAGE I                             4                             4
  STAGE II                           17                            17
  STAGE III                           7                            10
  STAGE IV                            7                            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  2(4P16.3) MUTATED    4 19  5  7
  AMP PEAK  2(4P16.3) WILD-TYPE  4 20  6 11
D2V4, multiclass
    clus
vv   AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE
  T1                           4                             4
  T2                          19                            20
  T3                           5                             6
  T4                           7                            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"
D2V5, binary
                               cls
clus                             0  1
  AMP PEAK  2(4P16.3) MUTATED   31  4
  AMP PEAK  2(4P16.3) WILD-TYPE 36  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(4P16.3) MUTATED     31    4
  AMP PEAK  2(4P16.3) WILD-TYPE   36    6
   clus
vv  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE
  0                          31                            36
  1                           4                             6
[1] 2 2
[1] FALSE
D2V6, binary
                               cls
clus                             0  1
  AMP PEAK  2(4P16.3) MUTATED   22 14
  AMP PEAK  2(4P16.3) WILD-TYPE 30 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(4P16.3) MUTATED     22   14
  AMP PEAK  2(4P16.3) WILD-TYPE   30   14
        clus
vv       AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE
  FEMALE                          22                            30
  MALE                            14                            14
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                             0  1
  AMP PEAK  2(4P16.3) MUTATED    4  8
  AMP PEAK  2(4P16.3) WILD-TYPE  4 19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(4P16.3) MUTATED      4    8
  AMP PEAK  2(4P16.3) WILD-TYPE    4   19
                        clus
vv                       AMP PEAK  2(4P16.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                           8
                        clus
vv                       AMP PEAK  2(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            19
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(4Q35.1) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  3(4Q35.1) MUTATED   20  6
  AMP PEAK  3(4Q35.1) WILD-TYPE 32 21
  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                           26                            53 
  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                            6                            21 
$`AMP PEAK  3(4Q35.1) MUTATED`
TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       12.00        38.89        57.53        40.34        46.82        41.26 
TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JZ 
       22.03        22.16       121.25        16.04        50.66         6.94 
TCGA-OR-A5K4 TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KZ TCGA-OR-A5LA TCGA-OR-A5LF 
       17.36        46.49       153.63         4.11        16.01        14.63 
TCGA-OR-A5LH TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO 
       78.41        73.05        53.03        61.08        62.99        64.08 
TCGA-OR-A5LT TCGA-OU-A5PI 
       12.00        23.31 

$`AMP PEAK  3(4Q35.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        30.31        18.12        91.46        69.21        41.39 
TCGA-OR-A5JG TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS 
       17.79        10.16        18.48        29.23         4.90        12.59 
TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K1 
        9.50        63.25        31.23        18.15        33.83        89.52 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT 
       32.68        93.44         8.32        37.15        11.31        87.88 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87        12.85       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LB TCGA-OR-A5LC 
       27.62        20.65        18.25        21.21        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LJ TCGA-OR-A5LP TCGA-OR-A5LR 
       39.35        21.76        52.24        36.33        52.04        21.01 
TCGA-OR-A5LS TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       29.00        12.59        10.09        27.29        42.51 

  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                         4.11                          4.90 
  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                       153.63                        128.12 
  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE 
                        40.80                         29.23 
[1] "4.1 - 153.6 (40.8)" "4.9 - 128.1 (29.2)"
[1] "hr=" "2"  
D3V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  3(4Q35.1) MUTATED         3       15         4        3
  AMP PEAK  3(4Q35.1) WILD-TYPE       5       19        13       14
D3V3, multiclass
           clus
vv          AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE
  STAGE I                             3                             5
  STAGE II                           15                            19
  STAGE III                           4                            13
  STAGE IV                            3                            14
[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(4Q35.1) MUTATED    3 16  2  4
  AMP PEAK  3(4Q35.1) WILD-TYPE  5 23  9 14
D3V4, multiclass
    clus
vv   AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE
  T1                           3                             5
  T2                          16                            23
  T3                           2                             9
  T4                           4                            14
[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"
D3V5, binary
                               cls
clus                             0  1
  AMP PEAK  3(4Q35.1) MUTATED   24  1
  AMP PEAK  3(4Q35.1) WILD-TYPE 43  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(4Q35.1) MUTATED     24    1
  AMP PEAK  3(4Q35.1) WILD-TYPE   43    9
   clus
vv  AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE
  0                          24                            43
  1                           1                             9
[1] 2 2
[1] FALSE
D3V6, binary
                               cls
clus                             0  1
  AMP PEAK  3(4Q35.1) MUTATED   15 11
  AMP PEAK  3(4Q35.1) WILD-TYPE 37 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(4Q35.1) MUTATED     15   11
  AMP PEAK  3(4Q35.1) WILD-TYPE   37   17
        clus
vv       AMP PEAK  3(4Q35.1) MUTATED AMP PEAK  3(4Q35.1) WILD-TYPE
  FEMALE                          15                            37
  MALE                            11                            17
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                             0  1
  AMP PEAK  3(4Q35.1) MUTATED    2  6
  AMP PEAK  3(4Q35.1) WILD-TYPE  6 21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(4Q35.1) MUTATED      2    6
  AMP PEAK  3(4Q35.1) WILD-TYPE    6   21
                        clus
vv                       AMP PEAK  3(4Q35.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                           6
                        clus
vv                       AMP PEAK  3(4Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            21
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(5P15.33) MUTATION ANALYSIS
D4V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  4(5P15.33) MUTATED   39 19
  AMP PEAK  4(5P15.33) WILD-TYPE 13  8
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            58                             21 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            19                              8 
$`AMP PEAK  4(5P15.33) MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        38.89        30.31        57.53        69.21        41.39 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       17.79        40.34        46.82        10.16        41.26        22.03 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY 
       22.16       121.25        16.04        50.66        63.25        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
        6.94        89.52        32.68        93.44        17.36         8.32 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       11.31        46.49       153.63        50.14        35.87         4.11 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       23.80        27.62        20.65        18.25        21.21        16.01 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
       39.58         5.23        14.63        52.24        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP 
       73.05        53.03        61.08        62.99        64.08        52.04 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       21.01        29.00        12.00        23.31 

$`AMP PEAK  4(5P15.33) WILD-TYPE`
TCGA-OR-A5J2 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       55.13        18.12        91.46        18.48        29.23         4.90 
TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JX TCGA-OR-A5K0 TCGA-OR-A5K6 TCGA-OR-A5KT 
       12.59         9.50        31.23        33.83        37.15        87.88 
TCGA-OR-A5KV TCGA-OR-A5KY TCGA-OR-A5L3 TCGA-OR-A5LD TCGA-OR-A5LE TCGA-P6-A5OG 
      120.30        12.85       128.12        39.35        21.76        12.59 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       10.09        27.29        42.51 

  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                          4.11                           4.90 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                        153.63                         128.12 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                        34.275                         29.230 
[1] "4.1 - 153.6 (34.3)" "4.9 - 128.1 (29.2)"
[1] "hr=" "1.3"
D4V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  4(5P15.33) MUTATED         5       28        13       12
  AMP PEAK  4(5P15.33) WILD-TYPE       3        6         4        5
D4V3, multiclass
           clus
vv          AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  STAGE I                              5                              3
  STAGE II                            28                              6
  STAGE III                           13                              4
  STAGE IV                            12                              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  4(5P15.33) MUTATED    5 32  8 13
  AMP PEAK  4(5P15.33) WILD-TYPE  3  7  3  5
D4V4, multiclass
    clus
vv   AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  T1                            5                              3
  T2                           32                              7
  T3                            8                              3
  T4                           13                              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"
D4V5, binary
                                cls
clus                              0  1
  AMP PEAK  4(5P15.33) MUTATED   50  8
  AMP PEAK  4(5P15.33) WILD-TYPE 17  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     50    8
  AMP PEAK  4(5P15.33) WILD-TYPE   17    2
   clus
vv  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  0                           50                             17
  1                            8                              2
[1] 2 2
[1] FALSE
D4V6, binary
                                cls
clus                              0  1
  AMP PEAK  4(5P15.33) MUTATED   38 21
  AMP PEAK  4(5P15.33) WILD-TYPE 14  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     38   21
  AMP PEAK  4(5P15.33) WILD-TYPE   14    7
        clus
vv       AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  FEMALE                           38                             14
  MALE                             21                              7
[1] 2 2
[1] FALSE
D4V7, binary
                                cls
clus                              0  1
  AMP PEAK  4(5P15.33) MUTATED    7 18
  AMP PEAK  4(5P15.33) WILD-TYPE  1  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED      7   18
  AMP PEAK  4(5P15.33) WILD-TYPE    1    9
                        clus
vv                       AMP PEAK  4(5P15.33) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           18
                        clus
vv                       AMP PEAK  4(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                              9
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(5Q35.3) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  5(5Q35.3) MUTATED   40 16
  AMP PEAK  5(5Q35.3) WILD-TYPE 12 11
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                           56                            23 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                           16                            11 
$`AMP PEAK  5(5Q35.3) MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       38.89        30.31        57.53        69.21        41.39        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ 
       40.34        46.82        10.16        41.26        22.03        22.16 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
      121.25        12.59        16.04        50.66        63.25        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO 
        6.94        89.52        93.44        17.36         8.32        46.49 
TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
      153.63        50.14        12.85        23.80        27.62        20.65 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LF 
       18.25        21.21        16.01        39.58         5.23        14.63 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       78.41        36.33        73.05        53.03        61.08        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       64.08        52.04        21.01        29.00        12.00        23.31 
TCGA-P6-A5OG TCGA-PK-A5HA 
       12.59        27.29 

$`AMP PEAK  5(5Q35.3) WILD-TYPE`
TCGA-OR-A5J2 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JM TCGA-OR-A5JO 
       55.13        19.04        18.12        91.46        18.48        29.23 
TCGA-OR-A5JP TCGA-OR-A5JU TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K6 
        4.90         9.50        18.15        33.83        32.68        37.15 
TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 
       11.31        87.88       120.30        35.87         4.11       128.12 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-PK-A5H9 TCGA-PK-A5HB 
       39.35        21.76        52.24        10.09        42.51 

  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                         5.23                          4.11 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                       153.63                        128.12 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                        30.77                         32.68 
[1] "5.2 - 153.6 (30.8)" "4.1 - 128.1 (32.7)"
[1] "hr=" "1.8"
D5V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  5(5Q35.3) MUTATED         5       27        10       13
  AMP PEAK  5(5Q35.3) WILD-TYPE       3        7         7        4
D5V3, multiclass
           clus
vv          AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE
  STAGE I                             5                             3
  STAGE II                           27                             7
  STAGE III                          10                             7
  STAGE IV                           13                             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(5Q35.3) MUTATED    5 30  7 13
  AMP PEAK  5(5Q35.3) WILD-TYPE  3  9  4  5
D5V4, multiclass
    clus
vv   AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE
  T1                           5                             3
  T2                          30                             9
  T3                           7                             4
  T4                          13                             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"
D5V5, binary
                               cls
clus                             0  1
  AMP PEAK  5(5Q35.3) MUTATED   49  7
  AMP PEAK  5(5Q35.3) WILD-TYPE 18  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.3) MUTATED     49    7
  AMP PEAK  5(5Q35.3) WILD-TYPE   18    3
   clus
vv  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE
  0                          49                            18
  1                           7                             3
[1] 2 2
[1] FALSE
D5V6, binary
                               cls
clus                             0  1
  AMP PEAK  5(5Q35.3) MUTATED   37 20
  AMP PEAK  5(5Q35.3) WILD-TYPE 15  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.3) MUTATED     37   20
  AMP PEAK  5(5Q35.3) WILD-TYPE   15    8
        clus
vv       AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE
  FEMALE                          37                            15
  MALE                            20                             8
[1] 2 2
[1] FALSE
D5V7, binary
                               cls
clus                             0  1
  AMP PEAK  5(5Q35.3) MUTATED    6 17
  AMP PEAK  5(5Q35.3) WILD-TYPE  2 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.3) MUTATED      6   17
  AMP PEAK  5(5Q35.3) WILD-TYPE    2   10
                        clus
vv                       AMP PEAK  5(5Q35.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          17
                        clus
vv                       AMP PEAK  5(5Q35.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            10
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(6P21.31) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  6(6P21.31) MUTATED    7  7
  AMP PEAK  6(6P21.31) WILD-TYPE 45 20
  AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(6P21.31) WILD-TYPE 
                            14                             65 
  AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(6P21.31) WILD-TYPE 
                             7                             20 
$`AMP PEAK  6(6P21.31) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE 
       15.45        79.82        16.11        30.31        57.53        69.21 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5KO TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5LK 
       22.03        18.48        46.49         4.11        23.80        73.05 
TCGA-OR-A5LM TCGA-OR-A5LN 
       61.08        62.99 

$`AMP PEAK  6(6P21.31) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5J9 
       44.55        55.13        63.85        12.00        19.04        38.89 
TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        91.46        41.39        17.79        40.34        46.82 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       10.16        41.26        29.23         4.90        22.16       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        16.04         9.50        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       18.15         6.94        33.83        89.52        32.68        93.44 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KU 
       17.36         8.32        37.15        11.31        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L3 TCGA-OR-A5L5 
      120.30        50.14        35.87        12.85       128.12        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       20.65        18.25        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
       39.35        21.76        14.63        52.24        78.41        36.33 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       53.03        64.08        52.04        21.01        29.00        12.00 
TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       23.31        12.59        10.09        27.29        42.51 

  AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(6P21.31) WILD-TYPE 
                          4.11                           4.90 
  AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(6P21.31) WILD-TYPE 
                         79.82                         153.63 
  AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(6P21.31) WILD-TYPE 
                         38.40                          31.23 
[1] "4.1 - 79.8 (38.4)"  "4.9 - 153.6 (31.2)"
[1] "hr=" "1.3"
D6V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  6(6P21.31) MUTATED         2        5         2        4
  AMP PEAK  6(6P21.31) WILD-TYPE       6       29        15       13
D6V3, multiclass
           clus
vv          AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(6P21.31) WILD-TYPE
  STAGE I                              2                              6
  STAGE II                             5                             29
  STAGE III                            2                             15
  STAGE IV                             4                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK  6(6P21.31) MUTATED    2  5  2  4
  AMP PEAK  6(6P21.31) WILD-TYPE  6 34  9 14
D6V4, multiclass
    clus
vv   AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(6P21.31) WILD-TYPE
  T1                            2                              6
  T2                            5                             34
  T3                            2                              9
  T4                            4                             14
[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"
D6V5, binary
                                cls
clus                              0  1
  AMP PEAK  6(6P21.31) MUTATED   12  1
  AMP PEAK  6(6P21.31) WILD-TYPE 55  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(6P21.31) MUTATED     12    1
  AMP PEAK  6(6P21.31) WILD-TYPE   55    9
   clus
vv  AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(6P21.31) WILD-TYPE
  0                           12                             55
  1                            1                              9
[1] 2 2
[1] FALSE
D6V6, binary
                                cls
clus                              0  1
  AMP PEAK  6(6P21.31) MUTATED   10  4
  AMP PEAK  6(6P21.31) WILD-TYPE 42 24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(6P21.31) MUTATED     10    4
  AMP PEAK  6(6P21.31) WILD-TYPE   42   24
        clus
vv       AMP PEAK  6(6P21.31) MUTATED AMP PEAK  6(6P21.31) WILD-TYPE
  FEMALE                           10                             42
  MALE                              4                             24
[1] 2 2
[1] FALSE
D6V7, binary
                                cls
clus                              0  1
  AMP PEAK  6(6P21.31) MUTATED    3  3
  AMP PEAK  6(6P21.31) WILD-TYPE  5 24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(6P21.31) MUTATED      3    3
  AMP PEAK  6(6P21.31) WILD-TYPE    5   24
                        clus
vv                       AMP PEAK  6(6P21.31) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                            3
                        clus
vv                       AMP PEAK  6(6P21.31) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             24
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(6Q24.3) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  7(6Q24.3) MUTATED    9  6
  AMP PEAK  7(6Q24.3) WILD-TYPE 43 21
  AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(6Q24.3) WILD-TYPE 
                           15                            64 
  AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(6Q24.3) WILD-TYPE 
                            6                            21 
$`AMP PEAK  7(6Q24.3) MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JL 
       79.82        19.04        30.31        57.53        69.21        22.03 
TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5KO TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5LK 
       33.83        32.68        46.49         4.11        23.80        73.05 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-PK-A5HA 
       61.08        62.99        27.29 

$`AMP PEAK  7(6Q24.3) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        12.00        16.11 
TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH 
       38.89        18.12        91.46        41.39        17.79        40.34 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       46.82        10.16        41.26        18.48        29.23         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
       22.16       121.25        12.59        16.04         9.50        50.66 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 
       63.25        31.23        18.15         6.94        89.52        93.44 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KU 
       17.36         8.32        37.15        11.31        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L3 TCGA-OR-A5L5 
      120.30        50.14        35.87        12.85       128.12        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       20.65        18.25        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
       39.35        21.76        14.63        52.24        78.41        36.33 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       53.03        64.08        52.04        21.01        29.00        12.00 
TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HB 
       23.31        12.59        10.09        42.51 

  AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(6Q24.3) WILD-TYPE 
                         4.11                          4.90 
  AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(6Q24.3) WILD-TYPE 
                        79.82                        153.63 
  AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(6Q24.3) WILD-TYPE 
                       33.830                        29.115 
[1] "4.1 - 79.8 (33.8)"  "4.9 - 153.6 (29.1)"
[1] "hr=" "1"  
D7V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  7(6Q24.3) MUTATED         2        6         3        2
  AMP PEAK  7(6Q24.3) WILD-TYPE       6       28        14       15
D7V3, multiclass
           clus
vv          AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(6Q24.3) WILD-TYPE
  STAGE I                             2                             6
  STAGE II                            6                            28
  STAGE III                           3                            14
  STAGE IV                            2                            15
[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(6Q24.3) MUTATED    2  6  1  4
  AMP PEAK  7(6Q24.3) WILD-TYPE  6 33 10 14
D7V4, multiclass
    clus
vv   AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(6Q24.3) WILD-TYPE
  T1                           2                             6
  T2                           6                            33
  T3                           1                            10
  T4                           4                            14
[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"
D7V5, binary
                               cls
clus                             0  1
  AMP PEAK  7(6Q24.3) MUTATED   14  0
  AMP PEAK  7(6Q24.3) WILD-TYPE 53 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(6Q24.3) MUTATED     14    0
  AMP PEAK  7(6Q24.3) WILD-TYPE   53   10
   clus
vv  AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(6Q24.3) WILD-TYPE
  0                          14                            53
  1                           0                            10
[1] 2 2
[1] FALSE
D7V6, binary
                               cls
clus                             0  1
  AMP PEAK  7(6Q24.3) MUTATED    9  6
  AMP PEAK  7(6Q24.3) WILD-TYPE 43 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(6Q24.3) MUTATED      9    6
  AMP PEAK  7(6Q24.3) WILD-TYPE   43   22
        clus
vv       AMP PEAK  7(6Q24.3) MUTATED AMP PEAK  7(6Q24.3) WILD-TYPE
  FEMALE                           9                            43
  MALE                             6                            22
[1] 2 2
[1] FALSE
D7V7, binary
                               cls
clus                             0  1
  AMP PEAK  7(6Q24.3) MUTATED    2  3
  AMP PEAK  7(6Q24.3) WILD-TYPE  6 24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(6Q24.3) MUTATED      2    3
  AMP PEAK  7(6Q24.3) WILD-TYPE    6   24
                        clus
vv                       AMP PEAK  7(6Q24.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       AMP PEAK  7(6Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            24
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(7P22.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  8(7P22.1) MUTATED   30 17
  AMP PEAK  8(7P22.1) WILD-TYPE 22 10
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                           47                            32 
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                           17                            10 
$`AMP PEAK  8(7P22.1) MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       55.13        63.85        12.00        79.82        16.11        19.04 
TCGA-OR-A5JA TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JJ TCGA-OR-A5JK 
       30.31        41.39        17.79        40.34        10.16        41.26 
TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX 
       22.03        22.16       121.25        16.04        50.66        31.23 
TCGA-OR-A5JY TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5KO 
       18.15        89.52        93.44         8.32        37.15        46.49 
TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L4 
      153.63        50.14        35.87        12.85         4.11        23.80 
TCGA-OR-A5L8 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       18.25        16.01        39.58         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       14.63        78.41        36.33        73.05        53.03        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LS TCGA-OU-A5PI 
       62.99        64.08        52.04        29.00        23.31 

$`AMP PEAK  8(7P22.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J4 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       44.55        15.45        38.89        18.12        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JI TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS 
       69.21        46.82        18.48        29.23         4.90        12.59 
TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K4 
        9.50        63.25         6.94        33.83        32.68        17.36 
TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 
       11.31        87.88       120.30       128.12        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LG TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PK-A5H9 
       21.21        52.24        21.01        12.00        12.59        10.09 
TCGA-PK-A5HA TCGA-PK-A5HB 
       27.29        42.51 

  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                         4.11                          4.90 
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                       153.63                        128.12 
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                       36.330                        27.455 
[1] "4.1 - 153.6 (36.3)" "4.9 - 128.1 (27.5)"
[1] "hr=" "1"  
D8V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  8(7P22.1) MUTATED         2       22        11       13
  AMP PEAK  8(7P22.1) WILD-TYPE       6       12         6        4
D8V3, multiclass
           clus
vv          AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE
  STAGE I                             2                             6
  STAGE II                           22                            12
  STAGE III                          11                             6
  STAGE IV                           13                             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  8(7P22.1) MUTATED    2 26  7 13
  AMP PEAK  8(7P22.1) WILD-TYPE  6 13  4  5
D8V4, multiclass
    clus
vv   AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE
  T1                           2                             6
  T2                          26                            13
  T3                           7                             4
  T4                          13                             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"
D8V5, binary
                               cls
clus                             0  1
  AMP PEAK  8(7P22.1) MUTATED   40  8
  AMP PEAK  8(7P22.1) WILD-TYPE 27  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P22.1) MUTATED     40    8
  AMP PEAK  8(7P22.1) WILD-TYPE   27    2
   clus
vv  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE
  0                          40                            27
  1                           8                             2
[1] 2 2
[1] FALSE
D8V6, binary
                               cls
clus                             0  1
  AMP PEAK  8(7P22.1) MUTATED   32 16
  AMP PEAK  8(7P22.1) WILD-TYPE 20 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P22.1) MUTATED     32   16
  AMP PEAK  8(7P22.1) WILD-TYPE   20   12
        clus
vv       AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE
  FEMALE                          32                            20
  MALE                            16                            12
[1] 2 2
[1] FALSE
D8V7, binary
                               cls
clus                             0  1
  AMP PEAK  8(7P22.1) MUTATED    6 18
  AMP PEAK  8(7P22.1) WILD-TYPE  2  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P22.1) MUTATED      6   18
  AMP PEAK  8(7P22.1) WILD-TYPE    2    9
                        clus
vv                       AMP PEAK  8(7P22.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          18
                        clus
vv                       AMP PEAK  8(7P22.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                             9
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(9Q31.3) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  9(9Q31.3) MUTATED   12 14
  AMP PEAK  9(9Q31.3) WILD-TYPE 40 13
  AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(9Q31.3) WILD-TYPE 
                           26                            53 
  AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(9Q31.3) WILD-TYPE 
                           14                            13 
$`AMP PEAK  9(9Q31.3) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA 
       15.45        12.00        16.11        19.04        38.89        30.31 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JJ TCGA-OR-A5JQ 
       69.21        41.39        17.79        40.34        10.16        22.16 
TCGA-OR-A5JV TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5KO TCGA-OR-A5KX TCGA-OR-A5KY 
       50.66        33.83        32.68        46.49        35.87        12.85 
TCGA-OR-A5KZ TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LS 
        4.11        39.58         5.23        36.33        53.03        29.00 
TCGA-OR-A5LT TCGA-OU-A5PI 
       12.00        23.31 

$`AMP PEAK  9(9Q31.3) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J6 TCGA-OR-A5JB TCGA-OR-A5JC 
       44.55        55.13        63.85        79.82        18.12        57.53 
TCGA-OR-A5JD TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       91.46        46.82        41.26        22.03        18.48        29.23 
TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW 
        4.90       121.25        12.59        16.04         9.50        63.25 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 
       31.23        18.15         6.94        89.52        93.44        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
        8.32        37.15        11.31        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       50.14       128.12        23.80        27.62        20.65        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       21.21        16.01        39.35        21.76        14.63        52.24 
TCGA-OR-A5LH TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP 
       78.41        73.05        61.08        62.99        64.08        52.04 
TCGA-OR-A5LR TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       21.01        12.59        10.09        27.29        42.51 

  AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(9Q31.3) WILD-TYPE 
                         4.11                          4.90 
  AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(9Q31.3) WILD-TYPE 
                        69.21                        153.63 
  AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(9Q31.3) WILD-TYPE 
                       29.655                        37.150 
[1] "4.1 - 69.2 (29.7)"  "4.9 - 153.6 (37.1)"
[1] "hr=" "3.6"
D9V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  9(9Q31.3) MUTATED         1        9         6       11
  AMP PEAK  9(9Q31.3) WILD-TYPE       7       25        11        6
D9V3, multiclass
           clus
vv          AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(9Q31.3) WILD-TYPE
  STAGE I                             1                             7
  STAGE II                            9                            25
  STAGE III                           6                            11
  STAGE IV                           11                             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
  AMP PEAK  9(9Q31.3) MUTATED    1 12  4 10
  AMP PEAK  9(9Q31.3) WILD-TYPE  7 27  7  8
D9V4, multiclass
    clus
vv   AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(9Q31.3) WILD-TYPE
  T1                           1                             7
  T2                          12                            27
  T3                           4                             7
  T4                          10                             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"
D9V5, binary
                               cls
clus                             0  1
  AMP PEAK  9(9Q31.3) MUTATED   20  7
  AMP PEAK  9(9Q31.3) WILD-TYPE 47  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(9Q31.3) MUTATED     20    7
  AMP PEAK  9(9Q31.3) WILD-TYPE   47    3
   clus
vv  AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(9Q31.3) WILD-TYPE
  0                          20                            47
  1                           7                             3
[1] 2 2
[1] FALSE
D9V6, binary
                               cls
clus                             0  1
  AMP PEAK  9(9Q31.3) MUTATED   19  8
  AMP PEAK  9(9Q31.3) WILD-TYPE 33 20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(9Q31.3) MUTATED     19    8
  AMP PEAK  9(9Q31.3) WILD-TYPE   33   20
        clus
vv       AMP PEAK  9(9Q31.3) MUTATED AMP PEAK  9(9Q31.3) WILD-TYPE
  FEMALE                          19                            33
  MALE                             8                            20
[1] 2 2
[1] FALSE
D9V7, binary
                               cls
clus                             0  1
  AMP PEAK  9(9Q31.3) MUTATED    5  9
  AMP PEAK  9(9Q31.3) WILD-TYPE  3 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(9Q31.3) MUTATED      5    9
  AMP PEAK  9(9Q31.3) WILD-TYPE    3   18
                        clus
vv                       AMP PEAK  9(9Q31.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                           9
                        clus
vv                       AMP PEAK  9(9Q31.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            18
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(12Q14.1) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 10(12Q14.1) MUTATED   40 21
  AMP PEAK 10(12Q14.1) WILD-TYPE 12  6
  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                            61                             18 
  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                            21                              6 
$`AMP PEAK 10(12Q14.1) MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        38.89        30.31        57.53        69.21        41.39 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       17.79        40.34        46.82        10.16        41.26        22.03 
TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       18.48         4.90        22.16       121.25        16.04        50.66 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       31.23        18.15         6.94        89.52        32.68        93.44 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW 
       17.36         8.32        11.31        87.88       153.63        50.14 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       35.87        12.85         4.11        23.80        27.62        20.65 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       18.25        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN 
       14.63        78.41        36.33        73.05        61.08        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       64.08        52.04        21.01        29.00        12.00        23.31 
TCGA-PK-A5HA 
       27.29 

$`AMP PEAK 10(12Q14.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JU 
       44.55        18.12        91.46        29.23        12.59         9.50 
TCGA-OR-A5JW TCGA-OR-A5K0 TCGA-OR-A5K6 TCGA-OR-A5KO TCGA-OR-A5KV TCGA-OR-A5L3 
       63.25        33.83        37.15        46.49       120.30       128.12 
TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LL TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HB 
       21.76        52.24        53.03        12.59        10.09        42.51 

  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                          4.11                           9.50 
  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                        153.63                         128.12 
  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE 
                         29.00                          39.83 
[1] "4.1 - 153.6 (29.0)" "9.5 - 128.1 (39.8)"
[1] "hr=" "1.1"
D10V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 10(12Q14.1) MUTATED         6       26        14       14
  AMP PEAK 10(12Q14.1) WILD-TYPE       2        8         3        3
D10V3, multiclass
           clus
vv          AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE
  STAGE I                              6                              2
  STAGE II                            26                              8
  STAGE III                           14                              3
  STAGE IV                            14                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 10(12Q14.1) MUTATED    6 30  9 15
  AMP PEAK 10(12Q14.1) WILD-TYPE  2  9  2  3
D10V4, multiclass
    clus
vv   AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE
  T1                            6                              2
  T2                           30                              9
  T3                            9                              2
  T4                           15                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
                                cls
clus                              0  1
  AMP PEAK 10(12Q14.1) MUTATED   52  9
  AMP PEAK 10(12Q14.1) WILD-TYPE 15  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(12Q14.1) MUTATED     52    9
  AMP PEAK 10(12Q14.1) WILD-TYPE   15    1
   clus
vv  AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE
  0                           52                             15
  1                            9                              1
[1] 2 2
[1] FALSE
D10V6, binary
                                cls
clus                              0  1
  AMP PEAK 10(12Q14.1) MUTATED   40 22
  AMP PEAK 10(12Q14.1) WILD-TYPE 12  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(12Q14.1) MUTATED     40   22
  AMP PEAK 10(12Q14.1) WILD-TYPE   12    6
        clus
vv       AMP PEAK 10(12Q14.1) MUTATED AMP PEAK 10(12Q14.1) WILD-TYPE
  FEMALE                           40                             12
  MALE                             22                              6
[1] 2 2
[1] FALSE
D10V7, binary
                                cls
clus                              0  1
  AMP PEAK 10(12Q14.1) MUTATED    8 19
  AMP PEAK 10(12Q14.1) WILD-TYPE  0  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(12Q14.1) MUTATED      8   19
  AMP PEAK 10(12Q14.1) WILD-TYPE    0    8
                        clus
vv                       AMP PEAK 10(12Q14.1) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           19
                        clus
vv                       AMP PEAK 10(12Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                              8
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(14Q11.2) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 11(14Q11.2) MUTATED   14  9
  AMP PEAK 11(14Q11.2) WILD-TYPE 38 18
  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                            23                             56 
  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                             9                             18 
$`AMP PEAK 11(14Q11.2) MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC 
       63.85        15.45        12.00        38.89        30.31        57.53 
TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JP 
       69.21        17.79        10.16        22.03        18.48         4.90 
TCGA-OR-A5KO TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LB 
       46.49        50.14        35.87        23.80        18.25        39.58 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OU-A5PI 
       53.03        61.08        64.08        29.00        23.31 

$`AMP PEAK 11(14Q11.2) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB 
       44.55        55.13        79.82        16.11        19.04        18.12 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JO 
       91.46        41.39        40.34        46.82        41.26        29.23 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
       22.16       121.25        12.59        16.04         9.50        50.66 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       63.25        31.23        18.15         6.94        33.83        89.52 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
       32.68        93.44        17.36         8.32        37.15        11.31 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 
       87.88       153.63       120.30        12.85         4.11       128.12 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       27.62        20.65        21.21        16.01         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       21.76        14.63        52.24        78.41        36.33        73.05 
TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PK-A5H9 
       62.99        52.04        21.01        12.00        12.59        10.09 
TCGA-PK-A5HA TCGA-PK-A5HB 
       27.29        42.51 

  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                          4.90                           4.11 
  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                         69.21                         153.63 
  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE 
                        30.310                         31.955 
[1] "4.9 - 69.2 (30.3)"  "4.1 - 153.6 (32.0)"
[1] "hr=" "1.3"
D11V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 11(14Q11.2) MUTATED         2        7         5        8
  AMP PEAK 11(14Q11.2) WILD-TYPE       6       27        12        9
D11V3, multiclass
           clus
vv          AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE
  STAGE I                              2                              6
  STAGE II                             7                             27
  STAGE III                            5                             12
  STAGE IV                             8                              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
  AMP PEAK 11(14Q11.2) MUTATED    2 10  2  8
  AMP PEAK 11(14Q11.2) WILD-TYPE  6 29  9 10
D11V4, multiclass
    clus
vv   AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE
  T1                            2                              6
  T2                           10                             29
  T3                            2                              9
  T4                            8                             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"
D11V5, binary
                                cls
clus                              0  1
  AMP PEAK 11(14Q11.2) MUTATED   16  6
  AMP PEAK 11(14Q11.2) WILD-TYPE 51  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(14Q11.2) MUTATED     16    6
  AMP PEAK 11(14Q11.2) WILD-TYPE   51    4
   clus
vv  AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE
  0                           16                             51
  1                            6                              4
[1] 2 2
[1] FALSE
D11V6, binary
                                cls
clus                              0  1
  AMP PEAK 11(14Q11.2) MUTATED   16  7
  AMP PEAK 11(14Q11.2) WILD-TYPE 36 21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(14Q11.2) MUTATED     16    7
  AMP PEAK 11(14Q11.2) WILD-TYPE   36   21
        clus
vv       AMP PEAK 11(14Q11.2) MUTATED AMP PEAK 11(14Q11.2) WILD-TYPE
  FEMALE                           16                             36
  MALE                              7                             21
[1] 2 2
[1] FALSE
D11V7, binary
                                cls
clus                              0  1
  AMP PEAK 11(14Q11.2) MUTATED    4  7
  AMP PEAK 11(14Q11.2) WILD-TYPE  4 20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(14Q11.2) MUTATED      4    7
  AMP PEAK 11(14Q11.2) WILD-TYPE    4   20
                        clus
vv                       AMP PEAK 11(14Q11.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                            7
                        clus
vv                       AMP PEAK 11(14Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             20
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(16P13.3) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 12(16P13.3) MUTATED   33 12
  AMP PEAK 12(16P13.3) WILD-TYPE 19 15
  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                            45                             34 
  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                            12                             15 
$`AMP PEAK 12(16P13.3) MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JA 
       44.55        63.85        15.45        12.00        38.89        30.31 
TCGA-OR-A5JC TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       57.53        41.39        17.79        40.34        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       41.26        22.03        22.16       121.25        16.04        50.66 
TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       31.23         6.94        89.52        93.44        17.36         8.32 
TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L4 
       46.49       153.63        50.14        12.85         4.11        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       27.62        20.65        18.25        21.21        16.01         5.23 
TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LP TCGA-OR-A5LR 
       39.35        14.63        53.03        61.08        52.04        21.01 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       29.00        12.00        23.31 

$`AMP PEAK 12(16P13.3) WILD-TYPE`
TCGA-OR-A5J2 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD 
       55.13        79.82        16.11        19.04        18.12        91.46 
TCGA-OR-A5JE TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JU 
       69.21        18.48        29.23         4.90        12.59         9.50 
TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K6 TCGA-OR-A5K9 
       63.25        18.15        33.83        32.68        37.15        11.31 
TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5LB TCGA-OR-A5LE 
       87.88       120.30        35.87       128.12        39.58        21.76 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LN TCGA-OR-A5LO 
       52.24        78.41        36.33        73.05        62.99        64.08 
TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       12.59        10.09        27.29        42.51 

  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                          4.11                           4.90 
  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                        153.63                         128.12 
  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE 
                         27.62                          36.10 
[1] "4.1 - 153.6 (27.6)" "4.9 - 128.1 (36.1)"
[1] "hr=" "1.3"
D12V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 12(16P13.3) MUTATED         4       21        10        9
  AMP PEAK 12(16P13.3) WILD-TYPE       4       13         7        8
D12V3, multiclass
           clus
vv          AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE
  STAGE I                              4                              4
  STAGE II                            21                             13
  STAGE III                           10                              7
  STAGE IV                             9                              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
  AMP PEAK 12(16P13.3) MUTATED    4 23  6 11
  AMP PEAK 12(16P13.3) WILD-TYPE  4 16  5  7
D12V4, multiclass
    clus
vv   AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE
  T1                            4                              4
  T2                           23                             16
  T3                            6                              5
  T4                           11                              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"
D12V5, binary
                                cls
clus                              0  1
  AMP PEAK 12(16P13.3) MUTATED   38  6
  AMP PEAK 12(16P13.3) WILD-TYPE 29  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(16P13.3) MUTATED     38    6
  AMP PEAK 12(16P13.3) WILD-TYPE   29    4
   clus
vv  AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE
  0                           38                             29
  1                            6                              4
[1] 2 2
[1] FALSE
D12V6, binary
                                cls
clus                              0  1
  AMP PEAK 12(16P13.3) MUTATED   27 18
  AMP PEAK 12(16P13.3) WILD-TYPE 25 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(16P13.3) MUTATED     27   18
  AMP PEAK 12(16P13.3) WILD-TYPE   25   10
        clus
vv       AMP PEAK 12(16P13.3) MUTATED AMP PEAK 12(16P13.3) WILD-TYPE
  FEMALE                           27                             25
  MALE                             18                             10
[1] 2 2
[1] FALSE
D12V7, binary
                                cls
clus                              0  1
  AMP PEAK 12(16P13.3) MUTATED    4 14
  AMP PEAK 12(16P13.3) WILD-TYPE  4 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(16P13.3) MUTATED      4   14
  AMP PEAK 12(16P13.3) WILD-TYPE    4   13
                        clus
vv                       AMP PEAK 12(16P13.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           14
                        clus
vv                       AMP PEAK 12(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             13
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(16Q22.1) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 13(16Q22.1) MUTATED   35 14
  AMP PEAK 13(16Q22.1) WILD-TYPE 17 13
  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                            49                             30 
  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                            14                             13 
$`AMP PEAK 13(16Q22.1) MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA 
       63.85        15.45        12.00        16.11        38.89        30.31 
TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
       57.53        69.21        41.39        17.79        40.34        46.82 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       10.16        41.26         4.90        22.16       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 
       50.66        31.23         6.94        89.52        93.44        17.36 
TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
       46.49       153.63        50.14        35.87        12.85         4.11 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       23.80        27.62        20.65        18.25        21.21        16.01 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LL TCGA-OR-A5LM 
        5.23        39.35        14.63        52.24        53.03        61.08 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       64.08        52.04        21.01        29.00        12.00        23.31 
TCGA-P6-A5OG 
       12.59 

$`AMP PEAK 13(16Q22.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD 
       44.55        55.13        79.82        19.04        18.12        91.46 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW 
       22.03        18.48        29.23        12.59         9.50        63.25 
TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
       18.15        33.83        32.68         8.32        37.15        11.31 
TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5L3 TCGA-OR-A5LB TCGA-OR-A5LE TCGA-OR-A5LH 
       87.88       120.30       128.12        39.58        21.76        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LN TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       36.33        73.05        62.99        10.09        27.29        42.51 

  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                          4.11                           8.32 
  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                        153.63                         128.12 
  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE 
                         29.00                          35.08 
[1] "4.1 - 153.6 (29.0)" "8.3 - 128.1 (35.1)"
[1] "hr=" "1.2"
D13V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 13(16Q22.1) MUTATED         4       22        12       11
  AMP PEAK 13(16Q22.1) WILD-TYPE       4       12         5        6
D13V3, multiclass
           clus
vv          AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE
  STAGE I                              4                              4
  STAGE II                            22                             12
  STAGE III                           12                              5
  STAGE IV                            11                              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
  AMP PEAK 13(16Q22.1) MUTATED    4 25  7 13
  AMP PEAK 13(16Q22.1) WILD-TYPE  4 14  4  5
D13V4, multiclass
    clus
vv   AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE
  T1                            4                              4
  T2                           25                             14
  T3                            7                              4
  T4                           13                              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"
D13V5, binary
                                cls
clus                              0  1
  AMP PEAK 13(16Q22.1) MUTATED   42  7
  AMP PEAK 13(16Q22.1) WILD-TYPE 25  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(16Q22.1) MUTATED     42    7
  AMP PEAK 13(16Q22.1) WILD-TYPE   25    3
   clus
vv  AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE
  0                           42                             25
  1                            7                              3
[1] 2 2
[1] FALSE
D13V6, binary
                                cls
clus                              0  1
  AMP PEAK 13(16Q22.1) MUTATED   31 19
  AMP PEAK 13(16Q22.1) WILD-TYPE 21  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(16Q22.1) MUTATED     31   19
  AMP PEAK 13(16Q22.1) WILD-TYPE   21    9
        clus
vv       AMP PEAK 13(16Q22.1) MUTATED AMP PEAK 13(16Q22.1) WILD-TYPE
  FEMALE                           31                             21
  MALE                             19                              9
[1] 2 2
[1] FALSE
D13V7, binary
                                cls
clus                              0  1
  AMP PEAK 13(16Q22.1) MUTATED    5 18
  AMP PEAK 13(16Q22.1) WILD-TYPE  3  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(16Q22.1) MUTATED      5   18
  AMP PEAK 13(16Q22.1) WILD-TYPE    3    9
                        clus
vv                       AMP PEAK 13(16Q22.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           18
                        clus
vv                       AMP PEAK 13(16Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                              9
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(16Q24.2) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 14(16Q24.2) MUTATED   32 12
  AMP PEAK 14(16Q24.2) WILD-TYPE 20 15
  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                            44                             35 
  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                            12                             15 
$`AMP PEAK 14(16Q24.2) MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC 
       44.55        63.85        12.00        38.89        30.31        57.53 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        41.39        17.79        40.34        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX 
       41.26        22.16       121.25        16.04        50.66        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5KO TCGA-OR-A5KU 
        6.94        89.52        93.44        17.36        46.49       153.63 
TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       50.14        12.85         4.11        23.80        27.62        20.65 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LL 
       18.25        21.21        16.01         5.23        14.63        53.03 
TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       61.08        64.08        52.04        21.01        29.00        12.00 
TCGA-OU-A5PI TCGA-P6-A5OG 
       23.31        12.59 

$`AMP PEAK 14(16Q24.2) WILD-TYPE`
TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB 
       55.13        15.45        79.82        16.11        19.04        18.12 
TCGA-OR-A5JD TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS 
       91.46        22.03        18.48        29.23         4.90        12.59 
TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K5 
        9.50        63.25        18.15        33.83        32.68         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5L3 
       37.15        11.31        87.88       120.30        35.87       128.12 
TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
       39.58        39.35        21.76        52.24        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LN TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       73.05        62.99        10.09        27.29        42.51 

  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                          4.11                           4.90 
  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                        153.63                         128.12 
  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE 
                        29.655                         33.830 
[1] "4.1 - 153.6 (29.7)" "4.9 - 128.1 (33.8)"
[1] "hr=" "1.5"
D14V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 14(16Q24.2) MUTATED         4       22         8        9
  AMP PEAK 14(16Q24.2) WILD-TYPE       4       12         9        8
D14V3, multiclass
           clus
vv          AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE
  STAGE I                              4                              4
  STAGE II                            22                             12
  STAGE III                            8                              9
  STAGE IV                             9                              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
  AMP PEAK 14(16Q24.2) MUTATED    4 24  4 11
  AMP PEAK 14(16Q24.2) WILD-TYPE  4 15  7  7
D14V4, multiclass
    clus
vv   AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE
  T1                            4                              4
  T2                           24                             15
  T3                            4                              7
  T4                           11                              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"
D14V5, binary
                                cls
clus                              0  1
  AMP PEAK 14(16Q24.2) MUTATED   38  5
  AMP PEAK 14(16Q24.2) WILD-TYPE 29  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(16Q24.2) MUTATED     38    5
  AMP PEAK 14(16Q24.2) WILD-TYPE   29    5
   clus
vv  AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE
  0                           38                             29
  1                            5                              5
[1] 2 2
[1] FALSE
D14V6, binary
                                cls
clus                              0  1
  AMP PEAK 14(16Q24.2) MUTATED   27 17
  AMP PEAK 14(16Q24.2) WILD-TYPE 25 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(16Q24.2) MUTATED     27   17
  AMP PEAK 14(16Q24.2) WILD-TYPE   25   11
        clus
vv       AMP PEAK 14(16Q24.2) MUTATED AMP PEAK 14(16Q24.2) WILD-TYPE
  FEMALE                           27                             25
  MALE                             17                             11
[1] 2 2
[1] FALSE
D14V7, binary
                                cls
clus                              0  1
  AMP PEAK 14(16Q24.2) MUTATED    3 14
  AMP PEAK 14(16Q24.2) WILD-TYPE  5 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(16Q24.2) MUTATED      3   14
  AMP PEAK 14(16Q24.2) WILD-TYPE    5   13
                        clus
vv                       AMP PEAK 14(16Q24.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           14
                        clus
vv                       AMP PEAK 14(16Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             13
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(17Q25.3) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 15(17Q25.3) MUTATED    8  5
  AMP PEAK 15(17Q25.3) WILD-TYPE 44 22
  AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(17Q25.3) WILD-TYPE 
                            13                             66 
  AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(17Q25.3) WILD-TYPE 
                             5                             22 
$`AMP PEAK 15(17Q25.3) MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JH TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JY 
       19.04        40.34        18.48         4.90        22.16        18.15 
TCGA-OR-A5K6 TCGA-OR-A5KU TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LO TCGA-OR-A5LT 
       37.15       153.63        39.35        14.63        64.08        12.00 
TCGA-PK-A5HA 
       27.29 

$`AMP PEAK 15(17Q25.3) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        38.89        30.31        18.12        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       69.21        41.39        17.79        46.82        10.16        41.26 
TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU 
       22.03        29.23       121.25        12.59        16.04         9.50 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       50.66        63.25        31.23         6.94        33.83        89.52 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO 
       32.68        93.44        17.36         8.32        11.31        46.49 
TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
       87.88       120.30        50.14        35.87        12.85         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      128.12        23.80        27.62        20.65        18.25        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH 
       16.01        39.58         5.23        21.76        52.24        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LP 
       36.33        73.05        53.03        61.08        62.99        52.04 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HB 
       21.01        29.00        23.31        12.59        10.09        42.51 

  AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(17Q25.3) WILD-TYPE 
                          4.90                           4.11 
  AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(17Q25.3) WILD-TYPE 
                        153.63                         128.12 
  AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(17Q25.3) WILD-TYPE 
                        22.160                         33.255 
[1] "4.9 - 153.6 (22.2)" "4.1 - 128.1 (33.3)"
[1] "hr=" "1.4"
D15V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 15(17Q25.3) MUTATED         0        6         4        3
  AMP PEAK 15(17Q25.3) WILD-TYPE       8       28        13       14
D15V3, multiclass
           clus
vv          AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(17Q25.3) WILD-TYPE
  STAGE I                              0                              8
  STAGE II                             6                             28
  STAGE III                            4                             13
  STAGE IV                             3                             14
[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 15(17Q25.3) MUTATED    0  6  3  4
  AMP PEAK 15(17Q25.3) WILD-TYPE  8 33  8 14
D15V4, multiclass
    clus
vv   AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(17Q25.3) WILD-TYPE
  T1                            0                              8
  T2                            6                             33
  T3                            3                              8
  T4                            4                             14
[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"
D15V5, binary
                                cls
clus                              0  1
  AMP PEAK 15(17Q25.3) MUTATED   13  1
  AMP PEAK 15(17Q25.3) WILD-TYPE 54  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(17Q25.3) MUTATED     13    1
  AMP PEAK 15(17Q25.3) WILD-TYPE   54    9
   clus
vv  AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(17Q25.3) WILD-TYPE
  0                           13                             54
  1                            1                              9
[1] 2 2
[1] FALSE
D15V6, binary
                                cls
clus                              0  1
  AMP PEAK 15(17Q25.3) MUTATED    9  5
  AMP PEAK 15(17Q25.3) WILD-TYPE 43 23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(17Q25.3) MUTATED      9    5
  AMP PEAK 15(17Q25.3) WILD-TYPE   43   23
        clus
vv       AMP PEAK 15(17Q25.3) MUTATED AMP PEAK 15(17Q25.3) WILD-TYPE
  FEMALE                            9                             43
  MALE                              5                             23
[1] 2 2
[1] FALSE
D15V7, binary
                                cls
clus                              0  1
  AMP PEAK 15(17Q25.3) MUTATED    1  4
  AMP PEAK 15(17Q25.3) WILD-TYPE  7 23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(17Q25.3) MUTATED      1    4
  AMP PEAK 15(17Q25.3) WILD-TYPE    7   23
                        clus
vv                       AMP PEAK 15(17Q25.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            4
                        clus
vv                       AMP PEAK 15(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                             23
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(19P13.12) MUTATION ANALYSIS
D16V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 16(19P13.12) MUTATED   30 20
  AMP PEAK 16(19P13.12) WILD-TYPE 22  7
  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                             50                              29 
  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                             20                               7 
$`AMP PEAK 16(19P13.12) MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       38.89        30.31        57.53        69.21        41.39        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP 
       40.34        46.82        10.16        41.26        18.48         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5K0 TCGA-OR-A5K2 
       22.16       121.25        50.66        31.23        33.83        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KW 
       93.44         8.32        11.31        46.49       153.63        50.14 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LB 
       35.87        12.85         4.11        23.80        18.25        39.58 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
        5.23        39.35        14.63        78.41        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LS 
       53.03        61.08        62.99        64.08        52.04        29.00 
TCGA-OR-A5LT TCGA-OU-A5PI 
       12.00        23.31 

$`AMP PEAK 16(19P13.12) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JL TCGA-OR-A5JO 
       44.55        19.04        18.12        91.46        22.03        29.23 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ 
       12.59        16.04         9.50        63.25        18.15         6.94 
TCGA-OR-A5K1 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5L3 
       89.52        17.36        37.15        87.88       120.30       128.12 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LE TCGA-OR-A5LG 
       27.62        20.65        21.21        16.01        21.76        52.24 
TCGA-OR-A5LR TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       21.01        12.59        10.09        27.29        42.51 

  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                           4.11                            6.94 
  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                         153.63                          128.12 
  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE 
                          37.61                           21.76 
[1] "4.1 - 153.6 (37.6)" "6.9 - 128.1 (21.8)"
[1] "hr=" "1.5"
D16V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 16(19P13.12) MUTATED         3       21        12       14
  AMP PEAK 16(19P13.12) WILD-TYPE       5       13         5        3
D16V3, multiclass
           clus
vv          AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE
  STAGE I                               3                               5
  STAGE II                             21                              13
  STAGE III                            12                               5
  STAGE IV                             14                               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T1 T2 T3 T4
  AMP PEAK 16(19P13.12) MUTATED    3 25  8 14
  AMP PEAK 16(19P13.12) WILD-TYPE  5 14  3  4
D16V4, multiclass
    clus
vv   AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE
  T1                             3                               5
  T2                            25                              14
  T3                             8                               3
  T4                            14                               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"
D16V5, binary
                                 cls
clus                               0  1
  AMP PEAK 16(19P13.12) MUTATED   42  8
  AMP PEAK 16(19P13.12) WILD-TYPE 25  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(19P13.12) MUTATED     42    8
  AMP PEAK 16(19P13.12) WILD-TYPE   25    2
   clus
vv  AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE
  0                            42                              25
  1                             8                               2
[1] 2 2
[1] FALSE
D16V6, binary
                                 cls
clus                               0  1
  AMP PEAK 16(19P13.12) MUTATED   34 17
  AMP PEAK 16(19P13.12) WILD-TYPE 18 11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(19P13.12) MUTATED     34   17
  AMP PEAK 16(19P13.12) WILD-TYPE   18   11
        clus
vv       AMP PEAK 16(19P13.12) MUTATED AMP PEAK 16(19P13.12) WILD-TYPE
  FEMALE                            34                              18
  MALE                              17                              11
[1] 2 2
[1] FALSE
D16V7, binary
                                 cls
clus                               0  1
  AMP PEAK 16(19P13.12) MUTATED    7 15
  AMP PEAK 16(19P13.12) WILD-TYPE  1 12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(19P13.12) MUTATED      7   15
  AMP PEAK 16(19P13.12) WILD-TYPE    1   12
                        clus
vv                       AMP PEAK 16(19P13.12) MUTATED
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            15
                        clus
vv                       AMP PEAK 16(19P13.12) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                              12
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(19Q12) MUTATION ANALYSIS
D17V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 17(19Q12) MUTATED   27 20
  AMP PEAK 17(19Q12) WILD-TYPE 25  7
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                          47                           32 
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                          20                            7 
$`AMP PEAK 17(19Q12) MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF 
       16.11        38.89        30.31        57.53        69.21        41.39 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM 
       17.79        40.34        46.82        10.16        41.26        18.48 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5K2 
        4.90        22.16       121.25        50.66        31.23        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KX 
       93.44         8.32        11.31        46.49       153.63        35.87 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LB TCGA-OR-A5LC 
       12.85         4.11        23.80        18.25        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       39.35        78.41        36.33        73.05        53.03        61.08 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       64.08        52.04        29.00        12.00        23.31 

$`AMP PEAK 17(19Q12) WILD-TYPE`
TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JS 
       19.04        18.12        91.46        22.03        29.23        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 
       16.04         9.50        63.25        18.15         6.94        33.83 
TCGA-OR-A5K1 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW 
       89.52        17.36        37.15        87.88       120.30        50.14 
TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LE 
      128.12        27.62        20.65        21.21        16.01        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LN TCGA-OR-A5LR TCGA-P6-A5OG TCGA-PK-A5H9 
       14.63        52.24        62.99        21.01        12.59        10.09 
TCGA-PK-A5HA TCGA-PK-A5HB 
       27.29        42.51 

  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                        4.11                         6.94 
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                      153.63                       128.12 
  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE 
                      38.890                       21.895 
[1] "4.1 - 153.6 (38.9)" "6.9 - 128.1 (21.9)"
[1] "hr=" "1.8"
D17V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 17(19Q12) MUTATED         3       20        10       14
  AMP PEAK 17(19Q12) WILD-TYPE       5       14         7        3
D17V3, multiclass
           clus
vv          AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE
  STAGE I                            3                            5
  STAGE II                          20                           14
  STAGE III                         10                            7
  STAGE IV                          14                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T1 T2 T3 T4
  AMP PEAK 17(19Q12) MUTATED    3 23  7 14
  AMP PEAK 17(19Q12) WILD-TYPE  5 16  4  4
D17V4, multiclass
    clus
vv   AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE
  T1                          3                            5
  T2                         23                           16
  T3                          7                            4
  T4                         14                            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"
D17V5, binary
                              cls
clus                            0  1
  AMP PEAK 17(19Q12) MUTATED   40  7
  AMP PEAK 17(19Q12) WILD-TYPE 27  3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(19Q12) MUTATED     40    7
  AMP PEAK 17(19Q12) WILD-TYPE   27    3
   clus
vv  AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE
  0                         40                           27
  1                          7                            3
[1] 2 2
[1] FALSE
D17V6, binary
                              cls
clus                            0  1
  AMP PEAK 17(19Q12) MUTATED   30 18
  AMP PEAK 17(19Q12) WILD-TYPE 22 10
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(19Q12) MUTATED     30   18
  AMP PEAK 17(19Q12) WILD-TYPE   22   10
        clus
vv       AMP PEAK 17(19Q12) MUTATED AMP PEAK 17(19Q12) WILD-TYPE
  FEMALE                         30                           22
  MALE                           18                           10
[1] 2 2
[1] FALSE
D17V7, binary
                              cls
clus                            0  1
  AMP PEAK 17(19Q12) MUTATED    7 14
  AMP PEAK 17(19Q12) WILD-TYPE  1 13
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(19Q12) MUTATED      7   14
  AMP PEAK 17(19Q12) WILD-TYPE    1   13
                        clus
vv                       AMP PEAK 17(19Q12) MUTATED
  HISPANIC OR LATINO                              7
  NOT HISPANIC OR LATINO                         14
                        clus
vv                       AMP PEAK 17(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           13
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(XP11.22) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 18(XP11.22) MUTATED   27 15
  AMP PEAK 18(XP11.22) WILD-TYPE 25 12
  AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(XP11.22) WILD-TYPE 
                            42                             37 
  AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(XP11.22) WILD-TYPE 
                            15                             12 
$`AMP PEAK 18(XP11.22) MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ 
       19.04        38.89        30.31        69.21        41.39        10.16 
TCGA-OR-A5JL TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 
       22.03       121.25        16.04        18.15         6.94        33.83 
TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KV 
       89.52        93.44        17.36        46.49       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 
       50.14        12.85         4.11        23.80        27.62        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH 
       21.21        16.01        39.58        39.35        14.63        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT 
       36.33        61.08        64.08        52.04        21.01        12.00 

$`AMP PEAK 18(XP11.22) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH 
       44.55        18.12        57.53        91.46        17.79        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       46.82        41.26        18.48        29.23         4.90        22.16 
TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 
       12.59         9.50        50.66        63.25        31.23        32.68 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KX TCGA-OR-A5L3 
        8.32        37.15        11.31        87.88        35.87       128.12 
TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LK TCGA-OR-A5LL 
       20.65         5.23        21.76        52.24        73.05        53.03 
TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       62.99        29.00        23.31        12.59        10.09        27.29 
TCGA-PK-A5HB 
       42.51 

  AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(XP11.22) WILD-TYPE 
                          4.11                           4.90 
  AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(XP11.22) WILD-TYPE 
                        153.63                         128.12 
  AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(XP11.22) WILD-TYPE 
                         32.07                          31.23 
[1] "4.1 - 153.6 (32.1)" "4.9 - 128.1 (31.2)"
[1] "hr=" "1"  
D18V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 18(XP11.22) MUTATED         4       18        11        9
  AMP PEAK 18(XP11.22) WILD-TYPE       4       16         6        8
D18V3, multiclass
           clus
vv          AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(XP11.22) WILD-TYPE
  STAGE I                              4                              4
  STAGE II                            18                             16
  STAGE III                           11                              6
  STAGE IV                             9                              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
  AMP PEAK 18(XP11.22) MUTATED    4 21  7 10
  AMP PEAK 18(XP11.22) WILD-TYPE  4 18  4  8
D18V4, multiclass
    clus
vv   AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(XP11.22) WILD-TYPE
  T1                            4                              4
  T2                           21                             18
  T3                            7                              4
  T4                           10                              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"
D18V5, binary
                                cls
clus                              0  1
  AMP PEAK 18(XP11.22) MUTATED   35  7
  AMP PEAK 18(XP11.22) WILD-TYPE 32  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(XP11.22) MUTATED     35    7
  AMP PEAK 18(XP11.22) WILD-TYPE   32    3
   clus
vv  AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(XP11.22) WILD-TYPE
  0                           35                             32
  1                            7                              3
[1] 2 2
[1] FALSE
D18V6, binary
                                cls
clus                              0  1
  AMP PEAK 18(XP11.22) MUTATED   30 12
  AMP PEAK 18(XP11.22) WILD-TYPE 22 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(XP11.22) MUTATED     30   12
  AMP PEAK 18(XP11.22) WILD-TYPE   22   16
        clus
vv       AMP PEAK 18(XP11.22) MUTATED AMP PEAK 18(XP11.22) WILD-TYPE
  FEMALE                           30                             22
  MALE                             12                             16
[1] 2 2
[1] FALSE
D18V7, binary
                                cls
clus                              0  1
  AMP PEAK 18(XP11.22) MUTATED    8 15
  AMP PEAK 18(XP11.22) WILD-TYPE  0 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(XP11.22) MUTATED      8   15
  AMP PEAK 18(XP11.22) WILD-TYPE    0   12
                        clus
vv                       AMP PEAK 18(XP11.22) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           15
                        clus
vv                       AMP PEAK 18(XP11.22) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                             12
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(XQ28) MUTATION ANALYSIS
D19V1, survival
                             sevent
clus2                          0  1
  AMP PEAK 19(XQ28) MUTATED   28 11
  AMP PEAK 19(XQ28) WILD-TYPE 24 16
  AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE 
                         39                          40 
  AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE 
                         11                          16 
$`AMP PEAK 19(XQ28) MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J9 TCGA-OR-A5JE 
       55.13        63.85        12.00        79.82        38.89        69.21 
TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JY 
       41.39        10.16        22.03       121.25        16.04        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO 
        6.94        89.52        93.44        17.36         8.32        46.49 
TCGA-OR-A5KU TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L5 
      153.63        35.87        12.85         4.11        23.80        27.62 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LF 
       18.25        21.21        16.01        39.58        39.35        14.63 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP 
       78.41        36.33        73.05        61.08        64.08        52.04 
TCGA-OR-A5LR TCGA-OR-A5LT TCGA-PK-A5HB 
       21.01        12.00        42.51 

$`AMP PEAK 19(XQ28) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       44.55        15.45        16.11        19.04        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       57.53        91.46        17.79        40.34        46.82        41.26 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JU 
       18.48        29.23         4.90        22.16        12.59         9.50 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K6 
       50.66        63.25        31.23        33.83        32.68        37.15 
TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5L3 TCGA-OR-A5L6 
       11.31        87.88       120.30        50.14       128.12        20.65 
TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LS 
        5.23        21.76        52.24        53.03        62.99        29.00 
TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       23.31        12.59        10.09        27.29 

  AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE 
                       4.11                        4.90 
  AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE 
                     153.63                      128.12 
  AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE 
                      36.33                       29.77 
[1] "4.1 - 153.6 (36.3)" "4.9 - 128.1 (29.8)"
[1] "hr=" "1.6"
D19V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 19(XQ28) MUTATED         4       18         9        8
  AMP PEAK 19(XQ28) WILD-TYPE       4       16         8        9
D19V3, multiclass
           clus
vv          AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE
  STAGE I                           4                           4
  STAGE II                         18                          16
  STAGE III                         9                           8
  STAGE IV                          8                           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
  AMP PEAK 19(XQ28) MUTATED    4 20  5 10
  AMP PEAK 19(XQ28) WILD-TYPE  4 19  6  8
D19V4, multiclass
    clus
vv   AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE
  T1                         4                           4
  T2                        20                          19
  T3                         5                           6
  T4                        10                           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"
D19V5, binary
                             cls
clus                           0  1
  AMP PEAK 19(XQ28) MUTATED   34  5
  AMP PEAK 19(XQ28) WILD-TYPE 33  5
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 19(XQ28) MUTATED     34    5
  AMP PEAK 19(XQ28) WILD-TYPE   33    5
   clus
vv  AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE
  0                        34                          33
  1                         5                           5
[1] 2 2
[1] FALSE
D19V6, binary
                             cls
clus                           0  1
  AMP PEAK 19(XQ28) MUTATED   27 13
  AMP PEAK 19(XQ28) WILD-TYPE 25 15
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 19(XQ28) MUTATED     27   13
  AMP PEAK 19(XQ28) WILD-TYPE   25   15
        clus
vv       AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE
  FEMALE                        27                          25
  MALE                          13                          15
[1] 2 2
[1] FALSE
D19V7, binary
                             cls
clus                           0  1
  AMP PEAK 19(XQ28) MUTATED    5 15
  AMP PEAK 19(XQ28) WILD-TYPE  3 12
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 19(XQ28) MUTATED      5   15
  AMP PEAK 19(XQ28) WILD-TYPE    3   12
                        clus
vv                       AMP PEAK 19(XQ28) MUTATED AMP PEAK 19(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             5                           3
  NOT HISPANIC OR LATINO                        15                          12
[1] 2 2
[1] FALSE

Clustering(20) Variable = DEL PEAK  1(1P36.23) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.23) MUTATED   24 10
  DEL PEAK  1(1P36.23) WILD-TYPE 28 17
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            34                             45 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            10                             17 
$`DEL PEAK  1(1P36.23) MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       55.13        15.45        38.89        57.53        91.46        69.21 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP 
       40.34        46.82        10.16        41.26        18.48         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       22.16        12.59        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KX TCGA-OR-A5KZ 
       32.68         8.32        37.15        11.31        35.87         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LG TCGA-OR-A5LM TCGA-OR-A5LN 
      128.12        20.65         5.23        52.24        61.08        62.99 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PK-A5HA 
       29.00        12.00        23.31        27.29 

$`DEL PEAK  1(1P36.23) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       44.55        63.85        12.00        79.82        16.11        19.04 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JL TCGA-OR-A5JO 
       30.31        18.12        41.39        17.79        22.03        29.23 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
      121.25        16.04         9.50         6.94        33.83        89.52 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       93.44        17.36        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 
       50.14        12.85        23.80        27.62        18.25        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LH 
       16.01        39.58        39.35        21.76        14.63        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HB 
       12.59        10.09        42.51 

  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                          4.11                           6.94 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                        128.12                         153.63 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                        31.955                         30.310 
[1] "4.1 - 128.1 (32.0)" "6.9 - 153.6 (30.3)"
[1] "hr=" "1.1"
D20V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  1(1P36.23) MUTATED         3       15         6        9
  DEL PEAK  1(1P36.23) WILD-TYPE       5       19        11        8
D20V3, multiclass
           clus
vv          DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  STAGE I                              3                              5
  STAGE II                            15                             19
  STAGE III                            6                             11
  STAGE IV                             9                              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  1(1P36.23) MUTATED    3 17  6  7
  DEL PEAK  1(1P36.23) WILD-TYPE  5 22  5 11
D20V4, multiclass
    clus
vv   DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  T1                            3                              5
  T2                           17                             22
  T3                            6                              5
  T4                            7                             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"
D20V5, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED   29  5
  DEL PEAK  1(1P36.23) WILD-TYPE 38  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     29    5
  DEL PEAK  1(1P36.23) WILD-TYPE   38    5
   clus
vv  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  0                           29                             38
  1                            5                              5
[1] 2 2
[1] FALSE
D20V6, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED   21 14
  DEL PEAK  1(1P36.23) WILD-TYPE 31 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     21   14
  DEL PEAK  1(1P36.23) WILD-TYPE   31   14
        clus
vv       DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  FEMALE                           21                             31
  MALE                             14                             14
[1] 2 2
[1] FALSE
D20V7, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED    3  9
  DEL PEAK  1(1P36.23) WILD-TYPE  5 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      3    9
  DEL PEAK  1(1P36.23) WILD-TYPE    5   18
                        clus
vv                       DEL PEAK  1(1P36.23) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                            9
                        clus
vv                       DEL PEAK  1(1P36.23) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             18
[1] 2 2
[1] FALSE

Clustering(21) Variable = DEL PEAK  2(1Q43) MUTATION ANALYSIS
D21V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  2(1Q43) MUTATED   11  6
  DEL PEAK  2(1Q43) WILD-TYPE 41 21
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                         17                          62 
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                          6                          21 
$`DEL PEAK  2(1Q43) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH 
       15.45        19.04        30.31        57.53        91.46        40.34 
TCGA-OR-A5JI TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       46.82        22.03        22.16        63.25        31.23        18.15 
TCGA-OR-A5KT TCGA-OR-A5L6 TCGA-OR-A5LF TCGA-OR-A5LM TCGA-OU-A5PI 
       87.88        20.65        14.63        61.08        23.31 

$`DEL PEAK  2(1Q43) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        12.00        79.82        16.11 
TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JJ 
       38.89        18.12        69.21        41.39        17.79        10.16 
TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS 
       41.26        18.48        29.23         4.90       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       16.04         9.50        50.66         6.94        33.83        89.52 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
       32.68        93.44        17.36         8.32        37.15        11.31 
TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       46.49       153.63       120.30        50.14        35.87        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 
        4.11       128.12        23.80        27.62        18.25        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG 
       16.01        39.58         5.23        39.35        21.76        52.24 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO 
       78.41        36.33        73.05        53.03        62.99        64.08 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PK-A5H9 
       52.04        21.01        29.00        12.00        12.59        10.09 
TCGA-PK-A5HA TCGA-PK-A5HB 
       27.29        42.51 

  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                      14.63                        4.11 
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                      91.46                      153.63 
  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE 
                     30.310                      33.255 
[1] "14.6 - 91.5 (30.3)" "4.1 - 153.6 (33.3)"
[1] "hr=" "1.1"
D21V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  2(1Q43) MUTATED         3        6         3        4
  DEL PEAK  2(1Q43) WILD-TYPE       5       28        14       13
D21V3, multiclass
           clus
vv          DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE
  STAGE I                           3                           5
  STAGE II                          6                          28
  STAGE III                         3                          14
  STAGE IV                          4                          13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T1 T2 T3 T4
  DEL PEAK  2(1Q43) MUTATED    3  7  4  2
  DEL PEAK  2(1Q43) WILD-TYPE  5 32  7 16
D21V4, multiclass
    clus
vv   DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE
  T1                         3                           5
  T2                         7                          32
  T3                         4                           7
  T4                         2                          16
[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"
D21V5, binary
                             cls
clus                           0  1
  DEL PEAK  2(1Q43) MUTATED   13  3
  DEL PEAK  2(1Q43) WILD-TYPE 54  7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q43) MUTATED     13    3
  DEL PEAK  2(1Q43) WILD-TYPE   54    7
   clus
vv  DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE
  0                        13                          54
  1                         3                           7
[1] 2 2
[1] FALSE
D21V6, binary
                             cls
clus                           0  1
  DEL PEAK  2(1Q43) MUTATED   10  7
  DEL PEAK  2(1Q43) WILD-TYPE 42 21
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q43) MUTATED     10    7
  DEL PEAK  2(1Q43) WILD-TYPE   42   21
        clus
vv       DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE
  FEMALE                        10                          42
  MALE                           7                          21
[1] 2 2
[1] FALSE
D21V7, binary
                             cls
clus                           0  1
  DEL PEAK  2(1Q43) MUTATED    2  3
  DEL PEAK  2(1Q43) WILD-TYPE  6 24
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q43) MUTATED      2    3
  DEL PEAK  2(1Q43) WILD-TYPE    6   24
                        clus
vv                       DEL PEAK  2(1Q43) MUTATED DEL PEAK  2(1Q43) WILD-TYPE
  HISPANIC OR LATINO                             2                           6
  NOT HISPANIC OR LATINO                         3                          24
[1] 2 2
[1] FALSE

Clustering(22) Variable = DEL PEAK  3(2Q22.1) MUTATION ANALYSIS
D22V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  3(2Q22.1) MUTATED   14  3
  DEL PEAK  3(2Q22.1) WILD-TYPE 38 24
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           17                            62 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            3                            24 
$`DEL PEAK  3(2Q22.1) MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JL 
       30.31        57.53        91.46        40.34        41.26        22.03 
TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       22.16        12.59        50.66        63.25        31.23        18.15 
TCGA-OR-A5KU TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA 
      153.63        62.99        29.00        23.31        27.29 

$`DEL PEAK  3(2Q22.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF 
       16.11        19.04        38.89        18.12        69.21        41.39 
TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       17.79        46.82        10.16        18.48        29.23         4.90 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
      121.25        16.04         9.50         6.94        33.83        89.52 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
       32.68        93.44        17.36         8.32        37.15        11.31 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       46.49        87.88       120.30        50.14        35.87        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
        4.11       128.12        23.80        27.62        20.65        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       21.21        16.01        39.58         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       14.63        52.24        78.41        36.33        73.05        53.03 
TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OG 
       61.08        64.08        52.04        21.01        12.00        12.59 
TCGA-PK-A5H9 TCGA-PK-A5HB 
       10.09        42.51 

  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                        12.59                          4.11 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                       153.63                        128.12 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                       31.230                        30.955 
[1] "12.6 - 153.6 (31.2)" "4.1 - 128.1 (31.0)" 
[1] "hr=" "2.6"
D22V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  3(2Q22.1) MUTATED         1        9         1        4
  DEL PEAK  3(2Q22.1) WILD-TYPE       7       25        16       13
D22V3, multiclass
           clus
vv          DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  STAGE I                             1                             7
  STAGE II                            9                            25
  STAGE III                           1                            16
  STAGE IV                            4                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  3(2Q22.1) MUTATED    1 10  1  3
  DEL PEAK  3(2Q22.1) WILD-TYPE  7 29 10 15
D22V4, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T1                           1                             7
  T2                          10                            29
  T3                           1                            10
  T4                           3                            15
[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"
D22V5, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   14  2
  DEL PEAK  3(2Q22.1) WILD-TYPE 53  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     14    2
  DEL PEAK  3(2Q22.1) WILD-TYPE   53    8
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                          14                            53
  1                           2                             8
[1] 2 2
[1] FALSE
D22V6, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED   11  6
  DEL PEAK  3(2Q22.1) WILD-TYPE 41 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     11    6
  DEL PEAK  3(2Q22.1) WILD-TYPE   41   22
        clus
vv       DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  FEMALE                          11                            41
  MALE                             6                            22
[1] 2 2
[1] FALSE
D22V7, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q22.1) MUTATED    0  2
  DEL PEAK  3(2Q22.1) WILD-TYPE  8 25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      0    2
  DEL PEAK  3(2Q22.1) WILD-TYPE    8   25
                        clus
vv                       DEL PEAK  3(2Q22.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           2
                        clus
vv                       DEL PEAK  3(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                            25
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK  4(2Q37.3) MUTATION ANALYSIS
D23V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(2Q37.3) MUTATED   15  5
  DEL PEAK  4(2Q37.3) WILD-TYPE 37 22
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           20                            59 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                            5                            22 
$`DEL PEAK  4(2Q37.3) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH 
       15.45        38.89        30.31        57.53        91.46        40.34 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW 
       41.26        22.03        22.16        12.59        50.66        63.25 
TCGA-OR-A5JX TCGA-OR-A5K0 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LN TCGA-OR-A5LS 
       31.23        33.83        39.58         5.23        62.99        29.00 
TCGA-OU-A5PI TCGA-PK-A5HA 
       23.31        27.29 

$`DEL PEAK  4(2Q37.3) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JI 
       19.04        18.12        69.21        41.39        17.79        46.82 
TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT 
       10.16        18.48        29.23         4.90       121.25        16.04 
TCGA-OR-A5JU TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
        9.50        18.15         6.94        89.52        32.68        93.44 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       17.36         8.32        37.15        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       120.30        50.14        35.87        12.85         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      128.12        23.80        27.62        20.65        18.25        21.21 
TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH 
       16.01        39.35        21.76        14.63        52.24        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP 
       36.33        73.05        53.03        61.08        64.08        52.04 
TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HB 
       21.01        12.00        12.59        10.09        42.51 

  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                         5.23                          4.11 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                        91.46                        153.63 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                        32.53                         29.23 
[1] "5.2 - 91.5 (32.5)"  "4.1 - 153.6 (29.2)"
[1] "hr=" "1.5"
D23V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  4(2Q37.3) MUTATED         1       10         1        6
  DEL PEAK  4(2Q37.3) WILD-TYPE       7       24        16       11
D23V3, multiclass
           clus
vv          DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  STAGE I                             1                             7
  STAGE II                           10                            24
  STAGE III                           1                            16
  STAGE IV                            6                            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  4(2Q37.3) MUTATED    1 11  2  4
  DEL PEAK  4(2Q37.3) WILD-TYPE  7 28  9 14
D23V4, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  T1                           1                             7
  T2                          11                            28
  T3                           2                             9
  T4                           4                            14
[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"
D23V5, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.3) MUTATED   17  2
  DEL PEAK  4(2Q37.3) WILD-TYPE 50  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     17    2
  DEL PEAK  4(2Q37.3) WILD-TYPE   50    8
   clus
vv  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  0                          17                            50
  1                           2                             8
[1] 2 2
[1] FALSE
D23V6, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.3) MUTATED   13  7
  DEL PEAK  4(2Q37.3) WILD-TYPE 39 21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     13    7
  DEL PEAK  4(2Q37.3) WILD-TYPE   39   21
        clus
vv       DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  FEMALE                          13                            39
  MALE                             7                            21
[1] 2 2
[1] FALSE
D23V7, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.3) MUTATED    2  3
  DEL PEAK  4(2Q37.3) WILD-TYPE  6 24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      2    3
  DEL PEAK  4(2Q37.3) WILD-TYPE    6   24
                        clus
vv                       DEL PEAK  4(2Q37.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       DEL PEAK  4(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            24
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK  5(3Q13.31) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  5(3Q13.31) MUTATED   10 10
  DEL PEAK  5(3Q13.31) WILD-TYPE 42 17
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                            20                             59 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                            10                             17 
$`DEL PEAK  5(3Q13.31) MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JG 
       79.82        16.11        19.04        30.31        57.53        17.79 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K0 
       41.26        22.03         4.90        63.25        18.15        33.83 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LL 
       11.31        46.49        20.65         5.23        21.76        53.03 
TCGA-OR-A5LM TCGA-PK-A5HB 
       61.08        42.51 

$`DEL PEAK  5(3Q13.31) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J9 
       44.55        55.13        63.85        15.45        12.00        38.89 
TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        91.46        69.21        41.39        40.34        46.82 
TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       10.16        18.48        29.23        22.16       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
       16.04         9.50        50.66        31.23         6.94        89.52 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5KT 
       32.68        93.44        17.36         8.32        37.15        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       120.30        50.14        35.87        12.85         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      128.12        23.80        27.62        18.25        21.21        16.01 
TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
       39.58        39.35        14.63        52.24        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       73.05        62.99        64.08        52.04        21.01        29.00 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       12.00        23.31        12.59        10.09        27.29 

  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                          4.90                           4.11 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                         79.82                         153.63 
  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE 
                         26.17                          32.68 
[1] "4.9 - 79.8 (26.2)"  "4.1 - 153.6 (32.7)"
[1] "hr=" "1.9"
D24V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  5(3Q13.31) MUTATED         1        9         2        7
  DEL PEAK  5(3Q13.31) WILD-TYPE       7       25        15       10
D24V3, multiclass
           clus
vv          DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  STAGE I                              1                              7
  STAGE II                             9                             25
  STAGE III                            2                             15
  STAGE IV                             7                             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(3Q13.31) MUTATED    1  9  2  7
  DEL PEAK  5(3Q13.31) WILD-TYPE  7 30  9 11
D24V4, multiclass
    clus
vv   DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  T1                            1                              7
  T2                            9                             30
  T3                            2                              9
  T4                            7                             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"
D24V5, binary
                                cls
clus                              0  1
  DEL PEAK  5(3Q13.31) MUTATED   17  2
  DEL PEAK  5(3Q13.31) WILD-TYPE 50  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3Q13.31) MUTATED     17    2
  DEL PEAK  5(3Q13.31) WILD-TYPE   50    8
   clus
vv  DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  0                           17                             50
  1                            2                              8
[1] 2 2
[1] FALSE
D24V6, binary
                                cls
clus                              0  1
  DEL PEAK  5(3Q13.31) MUTATED   11 10
  DEL PEAK  5(3Q13.31) WILD-TYPE 41 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3Q13.31) MUTATED     11   10
  DEL PEAK  5(3Q13.31) WILD-TYPE   41   18
        clus
vv       DEL PEAK  5(3Q13.31) MUTATED DEL PEAK  5(3Q13.31) WILD-TYPE
  FEMALE                           11                             41
  MALE                             10                             18
[1] 2 2
[1] FALSE
D24V7, binary
                                cls
clus                              0  1
  DEL PEAK  5(3Q13.31) MUTATED    3  5
  DEL PEAK  5(3Q13.31) WILD-TYPE  5 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3Q13.31) MUTATED      3    5
  DEL PEAK  5(3Q13.31) WILD-TYPE    5   22
                        clus
vv                       DEL PEAK  5(3Q13.31) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                            5
                        clus
vv                       DEL PEAK  5(3Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             22
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK  6(4Q34.3) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(4Q34.3) MUTATED    8 10
  DEL PEAK  6(4Q34.3) WILD-TYPE 44 17
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           18                            61 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           10                            17 
$`DEL PEAK  6(4Q34.3) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP 
       15.45        16.11        18.12        41.26        18.48         4.90 
TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K6 TCGA-OR-A5K9 
       12.59        50.66        18.15        32.68        37.15        11.31 
TCGA-OR-A5KY TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LS TCGA-PK-A5HA TCGA-PK-A5HB 
       12.85         5.23        21.76        29.00        27.29        42.51 

$`DEL PEAK  6(4Q34.3) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 
       44.55        55.13        63.85        12.00        79.82        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF 
       38.89        30.31        57.53        91.46        69.21        41.39 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO 
       17.79        40.34        46.82        10.16        22.03        29.23 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX 
       22.16       121.25        16.04         9.50        63.25        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
        6.94        33.83        89.52        93.44        17.36         8.32 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       46.49        87.88       153.63       120.30        50.14        35.87 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
        4.11       128.12        23.80        27.62        20.65        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LG 
       21.21        16.01        39.58        39.35        14.63        52.24 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       78.41        36.33        73.05        53.03        61.08        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       64.08        52.04        21.01        12.00        23.31        12.59 
TCGA-PK-A5H9 
       10.09 

  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                         4.90                          4.11 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                        50.66                        153.63 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                       18.315                        38.890 
[1] "4.9 - 50.7 (18.3)"  "4.1 - 153.6 (38.9)"
[1] "hr=" "4.3"
D25V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  6(4Q34.3) MUTATED         0        7         2        8
  DEL PEAK  6(4Q34.3) WILD-TYPE       8       27        15        9
D25V3, multiclass
           clus
vv          DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  STAGE I                             0                             8
  STAGE II                            7                            27
  STAGE III                           2                            15
  STAGE IV                            8                             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  6(4Q34.3) MUTATED    0  7  2  8
  DEL PEAK  6(4Q34.3) WILD-TYPE  8 32  9 10
D25V4, multiclass
    clus
vv   DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  T1                           0                             8
  T2                           7                            32
  T3                           2                             9
  T4                           8                            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"
D25V5, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q34.3) MUTATED   15  3
  DEL PEAK  6(4Q34.3) WILD-TYPE 52  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED     15    3
  DEL PEAK  6(4Q34.3) WILD-TYPE   52    7
   clus
vv  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  0                          15                            52
  1                           3                             7
[1] 2 2
[1] FALSE
D25V6, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q34.3) MUTATED   12  7
  DEL PEAK  6(4Q34.3) WILD-TYPE 40 21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED     12    7
  DEL PEAK  6(4Q34.3) WILD-TYPE   40   21
        clus
vv       DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  FEMALE                          12                            40
  MALE                             7                            21
[1] 2 2
[1] FALSE
D25V7, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q34.3) MUTATED    2  5
  DEL PEAK  6(4Q34.3) WILD-TYPE  6 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED      2    5
  DEL PEAK  6(4Q34.3) WILD-TYPE    6   22
                        clus
vv                       DEL PEAK  6(4Q34.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                           5
                        clus
vv                       DEL PEAK  6(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            22
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK  7(4Q35.1) MUTATION ANALYSIS
D26V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  7(4Q35.1) MUTATED   11 11
  DEL PEAK  7(4Q35.1) WILD-TYPE 41 16
  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                           22                            57 
  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                           11                            16 
$`DEL PEAK  7(4Q35.1) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JK 
       15.45        16.11        18.12        57.53        69.21        41.26 
TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY 
       18.48         4.90        12.59        50.66        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5KW TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE 
       32.68         8.32        50.14        39.58         5.23        21.76 
TCGA-OR-A5LN TCGA-OR-A5LS TCGA-PK-A5HA TCGA-PK-A5HB 
       62.99        29.00        27.29        42.51 

$`DEL PEAK  7(4Q35.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 
       44.55        55.13        63.85        12.00        79.82        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH 
       38.89        30.31        91.46        41.39        17.79        40.34 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR 
       46.82        10.16        22.03        29.23        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       16.04         9.50        63.25         6.94        33.83        89.52 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       93.44        17.36        37.15        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 
      153.63       120.30        35.87        12.85         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       23.80        27.62        20.65        18.25        21.21        16.01 
TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       39.35        14.63        52.24        78.41        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT 
       53.03        61.08        64.08        52.04        21.01        12.00 
TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 
       23.31        12.59        10.09 

  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                         4.90                          4.11 
  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                        69.21                        153.63 
  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                       28.145                        35.870 
[1] "4.9 - 69.2 (28.1)"  "4.1 - 153.6 (35.9)"
[1] "hr=" "2.4"
D26V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  7(4Q35.1) MUTATED         1        6         5        8
  DEL PEAK  7(4Q35.1) WILD-TYPE       7       28        12        9
D26V3, multiclass
           clus
vv          DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE
  STAGE I                             1                             7
  STAGE II                            6                            28
  STAGE III                           5                            12
  STAGE IV                            8                             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  7(4Q35.1) MUTATED    1  7  4  8
  DEL PEAK  7(4Q35.1) WILD-TYPE  7 32  7 10
D26V4, multiclass
    clus
vv   DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE
  T1                           1                             7
  T2                           7                            32
  T3                           4                             7
  T4                           8                            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"
D26V5, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q35.1) MUTATED   18  3
  DEL PEAK  7(4Q35.1) WILD-TYPE 49  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q35.1) MUTATED     18    3
  DEL PEAK  7(4Q35.1) WILD-TYPE   49    7
   clus
vv  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE
  0                          18                            49
  1                           3                             7
[1] 2 2
[1] FALSE
D26V6, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q35.1) MUTATED   13 10
  DEL PEAK  7(4Q35.1) WILD-TYPE 39 18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q35.1) MUTATED     13   10
  DEL PEAK  7(4Q35.1) WILD-TYPE   39   18
        clus
vv       DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE
  FEMALE                          13                            39
  MALE                            10                            18
[1] 2 2
[1] FALSE
D26V7, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q35.1) MUTATED    2  5
  DEL PEAK  7(4Q35.1) WILD-TYPE  6 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q35.1) MUTATED      2    5
  DEL PEAK  7(4Q35.1) WILD-TYPE    6   22
                        clus
vv                       DEL PEAK  7(4Q35.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                           5
                        clus
vv                       DEL PEAK  7(4Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            22
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK  8(6P24.3) MUTATION ANALYSIS
D27V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(6P24.3) MUTATED   11  6
  DEL PEAK  8(6P24.3) WILD-TYPE 41 21
  DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE 
                           17                            62 
  DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE 
                            6                            21 
$`DEL PEAK  8(6P24.3) MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JP 
       19.04        91.46        17.79        40.34        41.26         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5K0 TCGA-OR-A5KT TCGA-OR-A5LC TCGA-OR-A5LE 
       22.16        50.66        33.83        87.88         5.23        21.76 
TCGA-OR-A5LL TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       53.03        29.00        12.00        23.31        12.59 

$`DEL PEAK  8(6P24.3) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JE 
       16.11        38.89        30.31        18.12        57.53        69.21 
TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       41.39        46.82        10.16        22.03        18.48        29.23 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX 
      121.25        12.59        16.04         9.50        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
       18.15         6.94        89.52        32.68        93.44        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KV 
        8.32        37.15        11.31        46.49       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
       50.14        35.87        12.85         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       27.62        20.65        18.25        21.21        16.01        39.58 
TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       39.35        14.63        52.24        78.41        36.33        73.05 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PK-A5H9 
       61.08        62.99        64.08        52.04        21.01        10.09 
TCGA-PK-A5HA TCGA-PK-A5HB 
       27.29        42.51 

  DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE 
                         4.90                          4.11 
  DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE 
                        91.46                        153.63 
  DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE 
                       23.310                        34.275 
[1] "4.9 - 91.5 (23.3)"  "4.1 - 153.6 (34.3)"
[1] "hr=" "1.2"
D27V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  8(6P24.3) MUTATED         1        9         2        6
  DEL PEAK  8(6P24.3) WILD-TYPE       7       25        15       11
D27V3, multiclass
           clus
vv          DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE
  STAGE I                             1                             7
  STAGE II                            9                            25
  STAGE III                           2                            15
  STAGE IV                            6                            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  8(6P24.3) MUTATED    1 10  2  5
  DEL PEAK  8(6P24.3) WILD-TYPE  7 29  9 13
D27V4, multiclass
    clus
vv   DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE
  T1                           1                             7
  T2                          10                            29
  T3                           2                             9
  T4                           5                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V5, binary
                               cls
clus                             0  1
  DEL PEAK  8(6P24.3) MUTATED   16  2
  DEL PEAK  8(6P24.3) WILD-TYPE 51  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(6P24.3) MUTATED     16    2
  DEL PEAK  8(6P24.3) WILD-TYPE   51    8
   clus
vv  DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE
  0                          16                            51
  1                           2                             8
[1] 2 2
[1] FALSE
D27V6, binary
                               cls
clus                             0  1
  DEL PEAK  8(6P24.3) MUTATED   11  7
  DEL PEAK  8(6P24.3) WILD-TYPE 41 21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(6P24.3) MUTATED     11    7
  DEL PEAK  8(6P24.3) WILD-TYPE   41   21
        clus
vv       DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE
  FEMALE                          11                            41
  MALE                             7                            21
[1] 2 2
[1] FALSE
D27V7, binary
                               cls
clus                             0  1
  DEL PEAK  8(6P24.3) MUTATED    1  6
  DEL PEAK  8(6P24.3) WILD-TYPE  7 21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(6P24.3) MUTATED      1    6
  DEL PEAK  8(6P24.3) WILD-TYPE    7   21
                        clus
vv                       DEL PEAK  8(6P24.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           6
                        clus
vv                       DEL PEAK  8(6P24.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            21
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK  9(6Q26) MUTATION ANALYSIS
D28V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  9(6Q26) MUTATED   11  8
  DEL PEAK  9(6Q26) WILD-TYPE 41 19
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                         19                          60 
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                          8                          19 
$`DEL PEAK  9(6Q26) MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JK 
       16.11        18.12        91.46        17.79        40.34        41.26 
TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 
       22.16        12.59        50.66        18.15        33.83        32.68 
TCGA-OR-A5KO TCGA-OR-A5LC TCGA-OR-A5LG TCGA-OR-A5LL TCGA-OR-A5LS TCGA-OU-A5PI 
       46.49         5.23        52.24        53.03        29.00        23.31 
TCGA-P6-A5OG 
       12.59 

$`DEL PEAK  9(6Q26) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        38.89        30.31        57.53        69.21        41.39 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       46.82        10.16        22.03        18.48        29.23         4.90 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ 
      121.25        16.04         9.50        63.25        31.23         6.94 
TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
       89.52        93.44        17.36         8.32        37.15        11.31 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       87.88       153.63       120.30        50.14        35.87        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
        4.11       128.12        23.80        27.62        20.65        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       21.21        16.01        39.58        39.35        21.76        14.63 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO 
       78.41        36.33        73.05        61.08        62.99        64.08 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       52.04        21.01        12.00        10.09        27.29        42.51 

  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                       5.23                        4.11 
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                      91.46                      153.63 
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                      29.00                       33.55 
[1] "5.2 - 91.5 (29.0)"  "4.1 - 153.6 (33.5)"
[1] "hr=" "1.6"
D28V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  9(6Q26) MUTATED         0        8         3        9
  DEL PEAK  9(6Q26) WILD-TYPE       8       26        14        8
D28V3, multiclass
           clus
vv          DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  STAGE I                           0                           8
  STAGE II                          8                          26
  STAGE III                         3                          14
  STAGE IV                          9                           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  9(6Q26) MUTATED    0  9  2  9
  DEL PEAK  9(6Q26) WILD-TYPE  8 30  9  9
D28V4, multiclass
    clus
vv   DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  T1                         0                           8
  T2                         9                          30
  T3                         2                           9
  T4                         9                           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"
D28V5, binary
                             cls
clus                           0  1
  DEL PEAK  9(6Q26) MUTATED   17  3
  DEL PEAK  9(6Q26) WILD-TYPE 50  7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(6Q26) MUTATED     17    3
  DEL PEAK  9(6Q26) WILD-TYPE   50    7
   clus
vv  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  0                        17                          50
  1                         3                           7
[1] 2 2
[1] FALSE
D28V6, binary
                             cls
clus                           0  1
  DEL PEAK  9(6Q26) MUTATED   15  5
  DEL PEAK  9(6Q26) WILD-TYPE 37 23
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(6Q26) MUTATED     15    5
  DEL PEAK  9(6Q26) WILD-TYPE   37   23
        clus
vv       DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  FEMALE                        15                          37
  MALE                           5                          23
[1] 2 2
[1] FALSE
D28V7, binary
                             cls
clus                           0  1
  DEL PEAK  9(6Q26) MUTATED    1  6
  DEL PEAK  9(6Q26) WILD-TYPE  7 21
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(6Q26) MUTATED      1    6
  DEL PEAK  9(6Q26) WILD-TYPE    7   21
                        clus
vv                       DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             1                           7
  NOT HISPANIC OR LATINO                         6                          21
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK 10(7Q32.3) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 10(7Q32.3) MUTATED    3  5
  DEL PEAK 10(7Q32.3) WILD-TYPE 49 22
  DEL PEAK 10(7Q32.3) MUTATED DEL PEAK 10(7Q32.3) WILD-TYPE 
                            8                            71 
  DEL PEAK 10(7Q32.3) MUTATED DEL PEAK 10(7Q32.3) WILD-TYPE 
                            5                            22 
$`DEL PEAK 10(7Q32.3) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JM TCGA-OR-A5K0 TCGA-OR-A5K6 
       15.45        57.53        69.21        18.48        33.83        37.15 
TCGA-OR-A5LD TCGA-OR-A5LT 
       39.35        12.00 

$`DEL PEAK 10(7Q32.3) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        38.89        30.31        18.12        91.46        41.39 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       17.79        40.34        46.82        10.16        41.26        22.03 
TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT 
       29.23         4.90        22.16       121.25        12.59        16.04 
TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ 
        9.50        50.66        63.25        31.23        18.15         6.94 
TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 
       89.52        32.68        93.44        17.36         8.32        11.31 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       46.49        87.88       153.63       120.30        50.14        35.87 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       12.85         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE 
       18.25        21.21        16.01        39.58         5.23        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       14.63        52.24        78.41        36.33        73.05        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        62.99        64.08        52.04        21.01        29.00 
TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       23.31        12.59        10.09        27.29        42.51 

  DEL PEAK 10(7Q32.3) MUTATED DEL PEAK 10(7Q32.3) WILD-TYPE 
                        12.00                          4.11 
  DEL PEAK 10(7Q32.3) MUTATED DEL PEAK 10(7Q32.3) WILD-TYPE 
                        69.21                        153.63 
  DEL PEAK 10(7Q32.3) MUTATED DEL PEAK 10(7Q32.3) WILD-TYPE 
                        35.49                         30.31 
[1] "12.0 - 69.2 (35.5)" "4.1 - 153.6 (30.3)"
[1] "hr=" "2.1"
D29V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 10(7Q32.3) MUTATED         1        2         2        2
  DEL PEAK 10(7Q32.3) WILD-TYPE       7       32        15       15
D29V3, multiclass
           clus
vv          DEL PEAK 10(7Q32.3) MUTATED DEL PEAK 10(7Q32.3) WILD-TYPE
  STAGE I                             1                             7
  STAGE II                            2                            32
  STAGE III                           2                            15
  STAGE IV                            2                            15
[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(7Q32.3) MUTATED    1  2  2  2
  DEL PEAK 10(7Q32.3) WILD-TYPE  7 37  9 16
D29V4, multiclass
    clus
vv   DEL PEAK 10(7Q32.3) MUTATED DEL PEAK 10(7Q32.3) WILD-TYPE
  T1                           1                             7
  T2                           2                            37
  T3                           2                             9
  T4                           2                            16
[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"
D29V5, binary
                               cls
clus                             0  1
  DEL PEAK 10(7Q32.3) MUTATED    6  1
  DEL PEAK 10(7Q32.3) WILD-TYPE 61  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(7Q32.3) MUTATED      6    1
  DEL PEAK 10(7Q32.3) WILD-TYPE   61    9
   clus
vv  DEL PEAK 10(7Q32.3) MUTATED DEL PEAK 10(7Q32.3) WILD-TYPE
  0                           6                            61
  1                           1                             9
[1] 2 2
[1] FALSE
D29V6, binary
                               cls
clus                             0  1
  DEL PEAK 10(7Q32.3) MUTATED    5  3
  DEL PEAK 10(7Q32.3) WILD-TYPE 47 25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(7Q32.3) MUTATED      5    3
  DEL PEAK 10(7Q32.3) WILD-TYPE   47   25
        clus
vv       DEL PEAK 10(7Q32.3) MUTATED DEL PEAK 10(7Q32.3) WILD-TYPE
  FEMALE                           5                            47
  MALE                             3                            25
[1] 2 2
[1] FALSE
D29V7, binary
                               cls
clus                             0  1
  DEL PEAK 10(7Q32.3) MUTATED    1  2
  DEL PEAK 10(7Q32.3) WILD-TYPE  7 25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(7Q32.3) MUTATED      1    2
  DEL PEAK 10(7Q32.3) WILD-TYPE    7   25
                        clus
vv                       DEL PEAK 10(7Q32.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           2
                        clus
vv                       DEL PEAK 10(7Q32.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            25
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK 11(9P23) MUTATION ANALYSIS
D30V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 11(9P23) MUTATED   11 10
  DEL PEAK 11(9P23) WILD-TYPE 41 17
  DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE 
                         21                          58 
  DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE 
                         10                          17 
$`DEL PEAK 11(9P23) MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JK TCGA-OR-A5JL 
       16.11        19.04        38.89        57.53        41.26        22.03 
TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5K0 
       18.48         4.90        12.59        50.66        18.15        33.83 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5LC TCGA-OR-A5LE 
       32.68         8.32         4.11       128.12         5.23        21.76 
TCGA-OR-A5LG TCGA-OR-A5LM TCGA-P6-A5OG 
       52.24        61.08        12.59 

$`DEL PEAK 11(9P23) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       30.31        18.12        91.46        69.21        41.39        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR 
       40.34        46.82        10.16        29.23        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
       16.04         9.50        63.25        31.23         6.94        89.52 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       93.44        17.36        37.15        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L4 
      153.63       120.30        50.14        35.87        12.85        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       27.62        20.65        18.25        21.21        16.01        39.58 
TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       39.35        14.63        78.41        36.33        73.05        53.03 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       62.99        64.08        52.04        21.01        29.00        12.00 
TCGA-OU-A5PI TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       23.31        10.09        27.29        42.51 

  DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE 
                       4.11                        6.94 
  DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE 
                     128.12                      153.63 
  DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE 
                      21.76                       36.10 
[1] "4.1 - 128.1 (21.8)" "6.9 - 153.6 (36.1)"
[1] "hr=" "2.2"
D30V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 11(9P23) MUTATED         2        8         5        5
  DEL PEAK 11(9P23) WILD-TYPE       6       26        12       12
D30V3, multiclass
           clus
vv          DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE
  STAGE I                           2                           6
  STAGE II                          8                          26
  STAGE III                         5                          12
  STAGE IV                          5                          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 11(9P23) MUTATED    2  8  4  6
  DEL PEAK 11(9P23) WILD-TYPE  6 31  7 12
D30V4, multiclass
    clus
vv   DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE
  T1                         2                           6
  T2                         8                          31
  T3                         4                           7
  T4                         6                          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"
D30V5, binary
                             cls
clus                           0  1
  DEL PEAK 11(9P23) MUTATED   19  1
  DEL PEAK 11(9P23) WILD-TYPE 48  9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(9P23) MUTATED     19    1
  DEL PEAK 11(9P23) WILD-TYPE   48    9
   clus
vv  DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE
  0                        19                          48
  1                         1                           9
[1] 2 2
[1] FALSE
D30V6, binary
                             cls
clus                           0  1
  DEL PEAK 11(9P23) MUTATED   12  9
  DEL PEAK 11(9P23) WILD-TYPE 40 19
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(9P23) MUTATED     12    9
  DEL PEAK 11(9P23) WILD-TYPE   40   19
        clus
vv       DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE
  FEMALE                        12                          40
  MALE                           9                          19
[1] 2 2
[1] FALSE
D30V7, binary
                             cls
clus                           0  1
  DEL PEAK 11(9P23) MUTATED    3  6
  DEL PEAK 11(9P23) WILD-TYPE  5 21
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(9P23) MUTATED      3    6
  DEL PEAK 11(9P23) WILD-TYPE    5   21
                        clus
vv                       DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE
  HISPANIC OR LATINO                             3                           5
  NOT HISPANIC OR LATINO                         6                          21
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK 12(9P21.3) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 12(9P21.3) MUTATED   13 11
  DEL PEAK 12(9P21.3) WILD-TYPE 39 16
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           24                            55 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           11                            16 
$`DEL PEAK 12(9P21.3) MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JK TCGA-OR-A5JL 
       16.11        19.04        38.89        57.53        41.26        22.03 
TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JY 
       18.48         4.90        12.59        16.04        50.66        18.15 
TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KZ 
       33.83        32.68         8.32        37.15        11.31         4.11 
TCGA-OR-A5L3 TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LM TCGA-P6-A5OG 
      128.12         5.23        21.76        52.24        61.08        12.59 

$`DEL PEAK 12(9P21.3) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       30.31        18.12        91.46        69.21        41.39        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR 
       40.34        46.82        10.16        29.23        22.16       121.25 
TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 
        9.50        63.25        31.23         6.94        89.52        93.44 
TCGA-OR-A5K4 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       17.36        46.49        87.88       153.63       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       35.87        12.85        23.80        27.62        20.65        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH 
       21.21        16.01        39.58        39.35        14.63        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP 
       36.33        73.05        53.03        62.99        64.08        52.04 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PK-A5H9 TCGA-PK-A5HA 
       21.01        29.00        12.00        23.31        10.09        27.29 
TCGA-PK-A5HB 
       42.51 

  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                         4.11                          6.94 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                       128.12                        153.63 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                        20.40                         36.33 
[1] "4.1 - 128.1 (20.4)" "6.9 - 153.6 (36.3)"
[1] "hr=" "2.4"
D31V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 12(9P21.3) MUTATED         2       11         5        5
  DEL PEAK 12(9P21.3) WILD-TYPE       6       23        12       12
D31V3, multiclass
           clus
vv          DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  STAGE I                             2                             6
  STAGE II                           11                            23
  STAGE III                           5                            12
  STAGE IV                            5                            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 12(9P21.3) MUTATED    2 11  4  6
  DEL PEAK 12(9P21.3) WILD-TYPE  6 28  7 12
D31V4, multiclass
    clus
vv   DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  T1                           2                             6
  T2                          11                            28
  T3                           4                             7
  T4                           6                            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"
D31V5, binary
                               cls
clus                             0  1
  DEL PEAK 12(9P21.3) MUTATED   22  1
  DEL PEAK 12(9P21.3) WILD-TYPE 45  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P21.3) MUTATED     22    1
  DEL PEAK 12(9P21.3) WILD-TYPE   45    9
   clus
vv  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  0                          22                            45
  1                           1                             9
[1] 2 2
[1] FALSE
D31V6, binary
                               cls
clus                             0  1
  DEL PEAK 12(9P21.3) MUTATED   15  9
  DEL PEAK 12(9P21.3) WILD-TYPE 37 19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P21.3) MUTATED     15    9
  DEL PEAK 12(9P21.3) WILD-TYPE   37   19
        clus
vv       DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  FEMALE                          15                            37
  MALE                             9                            19
[1] 2 2
[1] FALSE
D31V7, binary
                               cls
clus                             0  1
  DEL PEAK 12(9P21.3) MUTATED    3  7
  DEL PEAK 12(9P21.3) WILD-TYPE  5 20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P21.3) MUTATED      3    7
  DEL PEAK 12(9P21.3) WILD-TYPE    5   20
                        clus
vv                       DEL PEAK 12(9P21.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                           7
                        clus
vv                       DEL PEAK 12(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            20
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK 13(10Q23.1) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 13(10Q23.1) MUTATED    6  3
  DEL PEAK 13(10Q23.1) WILD-TYPE 46 24
  DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE 
                             9                             70 
  DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE 
                             3                             24 
$`DEL PEAK 13(10Q23.1) MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JS 
       30.31        17.79        40.34        22.03        22.16        12.59 
TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5L6 
       50.66        18.15        20.65 

$`DEL PEAK 13(10Q23.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        38.89        18.12        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM 
       69.21        41.39        46.82        10.16        41.26        18.48 
TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW 
       29.23         4.90       121.25        16.04         9.50        63.25 
TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       31.23         6.94        33.83        89.52        32.68        93.44 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       17.36         8.32        37.15        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       120.30        50.14        35.87        12.85         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      128.12        23.80        27.62        18.25        21.21        16.01 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       39.58         5.23        39.35        21.76        14.63        52.24 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       78.41        36.33        73.05        53.03        61.08        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       64.08        52.04        21.01        29.00        12.00        23.31 
TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       12.59        10.09        27.29        42.51 

  DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE 
                         12.59                           4.11 
  DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE 
                         50.66                         153.63 
  DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE 
                         22.03                          34.85 
[1] "12.6 - 50.7 (22.0)" "4.1 - 153.6 (34.8)"
[1] "hr=" "1.4"
D32V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 13(10Q23.1) MUTATED         1        5         0        3
  DEL PEAK 13(10Q23.1) WILD-TYPE       7       29        17       14
D32V3, multiclass
           clus
vv          DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE
  STAGE I                              1                              7
  STAGE II                             5                             29
  STAGE III                            0                             17
  STAGE IV                             3                             14
[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(10Q23.1) MUTATED    1  5  0  3
  DEL PEAK 13(10Q23.1) WILD-TYPE  7 34 11 15
D32V4, multiclass
    clus
vv   DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE
  T1                            1                              7
  T2                            5                             34
  T3                            0                             11
  T4                            3                             15
[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"
D32V5, binary
                                cls
clus                              0  1
  DEL PEAK 13(10Q23.1) MUTATED    7  2
  DEL PEAK 13(10Q23.1) WILD-TYPE 60  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q23.1) MUTATED      7    2
  DEL PEAK 13(10Q23.1) WILD-TYPE   60    8
   clus
vv  DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE
  0                            7                             60
  1                            2                              8
[1] 2 2
[1] FALSE
D32V6, binary
                                cls
clus                              0  1
  DEL PEAK 13(10Q23.1) MUTATED    6  3
  DEL PEAK 13(10Q23.1) WILD-TYPE 46 25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q23.1) MUTATED      6    3
  DEL PEAK 13(10Q23.1) WILD-TYPE   46   25
        clus
vv       DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE
  FEMALE                            6                             46
  MALE                              3                             25
[1] 2 2
[1] FALSE
D32V7, binary
                                cls
clus                              0  1
  DEL PEAK 13(10Q23.1) MUTATED    0  1
  DEL PEAK 13(10Q23.1) WILD-TYPE  8 26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q23.1) MUTATED      0    1
  DEL PEAK 13(10Q23.1) WILD-TYPE    8   26
                        clus
vv                       DEL PEAK 13(10Q23.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            1
                        clus
vv                       DEL PEAK 13(10Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                             26
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK 14(11P15.5) MUTATION ANALYSIS
D33V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 14(11P15.5) MUTATED   19  7
  DEL PEAK 14(11P15.5) WILD-TYPE 33 20
  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                            26                             53 
  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                             7                             20 
$`DEL PEAK 14(11P15.5) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH 
       15.45        30.31        57.53        91.46        17.79        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5JW 
       46.82        41.26        22.03        22.16        50.66        63.25 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KW TCGA-OR-A5L6 
       31.23        18.15        37.15        11.31        50.14        20.65 
TCGA-OR-A5LC TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
        5.23        61.08        62.99        29.00        12.00        23.31 
TCGA-PK-A5HA TCGA-PK-A5HB 
       27.29        42.51 

$`DEL PEAK 14(11P15.5) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ 
       19.04        38.89        18.12        69.21        41.39        10.16 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT 
       18.48        29.23         4.90       121.25        12.59        16.04 
TCGA-OR-A5JU TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
        9.50         6.94        33.83        89.52        32.68        93.44 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       17.36         8.32        46.49        87.88       153.63       120.30 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       35.87        12.85         4.11       128.12        23.80        27.62 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE 
       18.25        21.21        16.01        39.58        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       14.63        52.24        78.41        36.33        73.05        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OG TCGA-PK-A5H9 
       64.08        52.04        21.01        12.59        10.09 

  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                          5.23                           4.11 
  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                         91.46                         153.63 
  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                         30.77                          32.68 
[1] "5.2 - 91.5 (30.8)"  "4.1 - 153.6 (32.7)"
[1] "hr=" "1.3"
D33V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 14(11P15.5) MUTATED         2       11         3        7
  DEL PEAK 14(11P15.5) WILD-TYPE       6       23        14       10
D33V3, multiclass
           clus
vv          DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE
  STAGE I                              2                              6
  STAGE II                            11                             23
  STAGE III                            3                             14
  STAGE IV                             7                             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 14(11P15.5) MUTATED    2 13  3  5
  DEL PEAK 14(11P15.5) WILD-TYPE  6 26  8 13
D33V4, multiclass
    clus
vv   DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE
  T1                            2                              6
  T2                           13                             26
  T3                            3                              8
  T4                            5                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V5, binary
                                cls
clus                              0  1
  DEL PEAK 14(11P15.5) MUTATED   19  5
  DEL PEAK 14(11P15.5) WILD-TYPE 48  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11P15.5) MUTATED     19    5
  DEL PEAK 14(11P15.5) WILD-TYPE   48    5
   clus
vv  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE
  0                           19                             48
  1                            5                              5
[1] 2 2
[1] FALSE
D33V6, binary
                                cls
clus                              0  1
  DEL PEAK 14(11P15.5) MUTATED   14 12
  DEL PEAK 14(11P15.5) WILD-TYPE 38 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11P15.5) MUTATED     14   12
  DEL PEAK 14(11P15.5) WILD-TYPE   38   16
        clus
vv       DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE
  FEMALE                           14                             38
  MALE                             12                             16
[1] 2 2
[1] FALSE
D33V7, binary
                                cls
clus                              0  1
  DEL PEAK 14(11P15.5) MUTATED    1  5
  DEL PEAK 14(11P15.5) WILD-TYPE  7 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11P15.5) MUTATED      1    5
  DEL PEAK 14(11P15.5) WILD-TYPE    7   22
                        clus
vv                       DEL PEAK 14(11P15.5) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            5
                        clus
vv                       DEL PEAK 14(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                             22
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK 15(11Q14.1) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 15(11Q14.1) MUTATED   17  6
  DEL PEAK 15(11Q14.1) WILD-TYPE 35 21
  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                            23                             56 
  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                             6                             21 
$`DEL PEAK 15(11Q14.1) MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH 
       19.04        30.31        57.53        91.46        17.79        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV 
       46.82        41.26        22.03        22.16        12.59        50.66 
TCGA-OR-A5JW TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LM 
       63.25        37.15        11.31        20.65         5.23        61.08 
TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA TCGA-PK-A5HB 
       62.99        29.00        23.31        27.29        42.51 

$`DEL PEAK 15(11Q14.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ 
       16.11        38.89        18.12        69.21        41.39        10.16 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU 
       18.48        29.23         4.90       121.25        16.04         9.50 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 
       31.23        18.15         6.94        33.83        89.52        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       93.44        17.36         8.32        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 
      120.30        50.14        35.87        12.85         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       23.80        27.62        18.25        21.21        16.01        39.58 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
       39.35        21.76        14.63        52.24        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT 
       73.05        53.03        64.08        52.04        21.01        12.00 
TCGA-P6-A5OG TCGA-PK-A5H9 
       12.59        10.09 

  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                          5.23                           4.11 
  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                         91.46                         153.63 
  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                        30.310                         31.955 
[1] "5.2 - 91.5 (30.3)"  "4.1 - 153.6 (32.0)"
[1] "hr=" "1.4"
D34V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 15(11Q14.1) MUTATED         2       12         1        5
  DEL PEAK 15(11Q14.1) WILD-TYPE       6       22        16       12
D34V3, multiclass
           clus
vv          DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE
  STAGE I                              2                              6
  STAGE II                            12                             22
  STAGE III                            1                             16
  STAGE IV                             5                             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 15(11Q14.1) MUTATED    2 13  1  4
  DEL PEAK 15(11Q14.1) WILD-TYPE  6 26 10 14
D34V4, multiclass
    clus
vv   DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE
  T1                            2                              6
  T2                           13                             26
  T3                            1                             10
  T4                            4                             14
[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"
D34V5, binary
                                cls
clus                              0  1
  DEL PEAK 15(11Q14.1) MUTATED   19  2
  DEL PEAK 15(11Q14.1) WILD-TYPE 48  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q14.1) MUTATED     19    2
  DEL PEAK 15(11Q14.1) WILD-TYPE   48    8
   clus
vv  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE
  0                           19                             48
  1                            2                              8
[1] 2 2
[1] FALSE
D34V6, binary
                                cls
clus                              0  1
  DEL PEAK 15(11Q14.1) MUTATED   12 11
  DEL PEAK 15(11Q14.1) WILD-TYPE 40 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q14.1) MUTATED     12   11
  DEL PEAK 15(11Q14.1) WILD-TYPE   40   17
        clus
vv       DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE
  FEMALE                           12                             40
  MALE                             11                             17
[1] 2 2
[1] FALSE
D34V7, binary
                                cls
clus                              0  1
  DEL PEAK 15(11Q14.1) MUTATED    1  4
  DEL PEAK 15(11Q14.1) WILD-TYPE  7 23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q14.1) MUTATED      1    4
  DEL PEAK 15(11Q14.1) WILD-TYPE    7   23
                        clus
vv                       DEL PEAK 15(11Q14.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            4
                        clus
vv                       DEL PEAK 15(11Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                             23
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 16(12Q14.2) MUTATION ANALYSIS
D35V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 16(12Q14.2) MUTATED    1  4
  DEL PEAK 16(12Q14.2) WILD-TYPE 51 23
  DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE 
                             5                             74 
  DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE 
                             4                             23 
$`DEL PEAK 16(12Q14.2) MUTATED`
TCGA-OR-A5JB TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5LL TCGA-P6-A5OG 
       18.12        11.31        87.88        53.03        12.59 

$`DEL PEAK 16(12Q14.2) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        38.89        30.31        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        41.39        17.79        40.34        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       41.26        22.03        18.48        29.23         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW 
      121.25        12.59        16.04         9.50        50.66        63.25 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 
       31.23        18.15         6.94        33.83        89.52        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5KO TCGA-OR-A5KU 
       93.44        17.36         8.32        37.15        46.49       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 
      120.30        50.14        35.87        12.85         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       23.80        27.62        20.65        18.25        21.21        16.01 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       39.58         5.23        39.35        21.76        14.63        52.24 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO 
       78.41        36.33        73.05        61.08        62.99        64.08 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PK-A5H9 
       52.04        21.01        29.00        12.00        23.31        10.09 
TCGA-PK-A5HA TCGA-PK-A5HB 
       27.29        42.51 

  DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE 
                         11.31                           4.11 
  DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE 
                         87.88                         153.63 
  DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE 
                        18.120                         31.955 
[1] "11.3 - 87.9 (18.1)" "4.1 - 153.6 (32.0)"
[1] "hr=" "2.8"
D35V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 16(12Q14.2) MUTATED         1        2         0        2
  DEL PEAK 16(12Q14.2) WILD-TYPE       7       32        17       15
D35V3, multiclass
           clus
vv          DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE
  STAGE I                              1                              7
  STAGE II                             2                             32
  STAGE III                            0                             17
  STAGE IV                             2                             15
[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(12Q14.2) MUTATED    1  2  0  2
  DEL PEAK 16(12Q14.2) WILD-TYPE  7 37 11 16
D35V4, multiclass
    clus
vv   DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE
  T1                            1                              7
  T2                            2                             37
  T3                            0                             11
  T4                            2                             16
[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"
D35V5, binary
                                cls
clus                              0  1
  DEL PEAK 16(12Q14.2) MUTATED    5  0
  DEL PEAK 16(12Q14.2) WILD-TYPE 62 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(12Q14.2) MUTATED      5    0
  DEL PEAK 16(12Q14.2) WILD-TYPE   62   10
   clus
vv  DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE
  0                            5                             62
  1                            0                             10
[1] 2 2
[1] FALSE
D35V6, binary
                                cls
clus                              0  1
  DEL PEAK 16(12Q14.2) MUTATED    4  1
  DEL PEAK 16(12Q14.2) WILD-TYPE 48 27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(12Q14.2) MUTATED      4    1
  DEL PEAK 16(12Q14.2) WILD-TYPE   48   27
        clus
vv       DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE
  FEMALE                            4                             48
  MALE                              1                             27
[1] 2 2
[1] FALSE
D35V7, binary
                                cls
clus                              0  1
  DEL PEAK 16(12Q14.2) MUTATED    0  2
  DEL PEAK 16(12Q14.2) WILD-TYPE  8 25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(12Q14.2) MUTATED      0    2
  DEL PEAK 16(12Q14.2) WILD-TYPE    8   25
                        clus
vv                       DEL PEAK 16(12Q14.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            2
                        clus
vv                       DEL PEAK 16(12Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                             25
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 17(13Q14.2) MUTATION ANALYSIS
D36V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 17(13Q14.2) MUTATED   20 15
  DEL PEAK 17(13Q14.2) WILD-TYPE 32 12
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                            35                             44 
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                            15                             12 
$`DEL PEAK 17(13Q14.2) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       15.45        16.11        30.31        18.12        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP 
       69.21        17.79        40.34        46.82        41.26         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY 
       22.16        12.59         9.50        50.66        63.25        18.15 
TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KU 
       33.83        32.68         8.32        11.31        46.49       153.63 
TCGA-OR-A5KZ TCGA-OR-A5L6 TCGA-OR-A5LD TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN 
        4.11        20.65        39.35        73.05        53.03        62.99 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5HA TCGA-PK-A5HB 
       29.00        23.31        12.59        27.29        42.51 

$`DEL PEAK 17(13Q14.2) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 
       44.55        55.13        63.85        12.00        79.82        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       38.89        41.39        10.16        22.03        18.48        29.23 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 
      121.25        16.04        31.23         6.94        89.52        93.44 
TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       17.36        37.15        87.88       120.30        50.14        35.87 
TCGA-OR-A5KY TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 
       12.85       128.12        23.80        27.62        18.25        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       16.01        39.58         5.23        21.76        14.63        52.24 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       78.41        36.33        61.08        64.08        52.04        21.01 
TCGA-OR-A5LT TCGA-PK-A5H9 
       12.00        10.09 

  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                          4.11                           5.23 
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                        153.63                         128.12 
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                         30.31                          33.55 
[1] "4.1 - 153.6 (30.3)" "5.2 - 128.1 (33.5)"
[1] "hr=" "1.8"
D36V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 17(13Q14.2) MUTATED         2       16         5       10
  DEL PEAK 17(13Q14.2) WILD-TYPE       6       18        12        7
D36V3, multiclass
           clus
vv          DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE
  STAGE I                              2                              6
  STAGE II                            16                             18
  STAGE III                            5                             12
  STAGE IV                            10                              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 17(13Q14.2) MUTATED    2 17  4 10
  DEL PEAK 17(13Q14.2) WILD-TYPE  6 22  7  8
D36V4, multiclass
    clus
vv   DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE
  T1                            2                              6
  T2                           17                             22
  T3                            4                              7
  T4                           10                              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"
D36V5, binary
                                cls
clus                              0  1
  DEL PEAK 17(13Q14.2) MUTATED   30  4
  DEL PEAK 17(13Q14.2) WILD-TYPE 37  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(13Q14.2) MUTATED     30    4
  DEL PEAK 17(13Q14.2) WILD-TYPE   37    6
   clus
vv  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE
  0                           30                             37
  1                            4                              6
[1] 2 2
[1] FALSE
D36V6, binary
                                cls
clus                              0  1
  DEL PEAK 17(13Q14.2) MUTATED   22 14
  DEL PEAK 17(13Q14.2) WILD-TYPE 30 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(13Q14.2) MUTATED     22   14
  DEL PEAK 17(13Q14.2) WILD-TYPE   30   14
        clus
vv       DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE
  FEMALE                           22                             30
  MALE                             14                             14
[1] 2 2
[1] FALSE
D36V7, binary
                                cls
clus                              0  1
  DEL PEAK 17(13Q14.2) MUTATED    2  8
  DEL PEAK 17(13Q14.2) WILD-TYPE  6 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(13Q14.2) MUTATED      2    8
  DEL PEAK 17(13Q14.2) WILD-TYPE    6   19
                        clus
vv                       DEL PEAK 17(13Q14.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                            8
                        clus
vv                       DEL PEAK 17(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             19
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 18(14Q21.2) MUTATION ANALYSIS
D37V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(14Q21.2) MUTATED   12  6
  DEL PEAK 18(14Q21.2) WILD-TYPE 40 21
  DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE 
                            18                             61 
  DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE 
                             6                             21 
$`DEL PEAK 18(14Q21.2) MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH 
       79.82        16.11        19.04        57.53        91.46        40.34 
TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5KO TCGA-OR-A5KZ TCGA-OR-A5L6 
       41.26        22.16        50.66        46.49         4.11        20.65 
TCGA-OR-A5LC TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PK-A5HA 
        5.23        62.99        29.00        12.00        12.59        27.29 

$`DEL PEAK 18(14Q21.2) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J9 
       44.55        55.13        63.85        15.45        12.00        38.89 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JI 
       30.31        18.12        69.21        41.39        17.79        46.82 
TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR 
       10.16        22.03        18.48        29.23         4.90       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       12.59        16.04         9.50        63.25        31.23        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
        6.94        33.83        89.52        32.68        93.44        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
        8.32        37.15        11.31        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        35.87        12.85       128.12        23.80        27.62 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE 
       18.25        21.21        16.01        39.58        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       14.63        52.24        78.41        36.33        73.05        53.03 
TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OU-A5PI TCGA-PK-A5H9 
       61.08        64.08        52.04        21.01        23.31        10.09 
TCGA-PK-A5HB 
       42.51 

  DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE 
                          4.11                           4.90 
  DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE 
                         91.46                         153.63 
  DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE 
                        28.145                         32.680 
[1] "4.1 - 91.5 (28.1)"  "4.9 - 153.6 (32.7)"
[1] "hr=" "1"  
D37V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 18(14Q21.2) MUTATED         0        9         3        4
  DEL PEAK 18(14Q21.2) WILD-TYPE       8       25        14       13
D37V3, multiclass
           clus
vv          DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE
  STAGE I                              0                              8
  STAGE II                             9                             25
  STAGE III                            3                             14
  STAGE IV                             4                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 18(14Q21.2) MUTATED    0  9  3  4
  DEL PEAK 18(14Q21.2) WILD-TYPE  8 30  8 14
D37V4, multiclass
    clus
vv   DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE
  T1                            0                              8
  T2                            9                             30
  T3                            3                              8
  T4                            4                             14
[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"
D37V5, binary
                                cls
clus                              0  1
  DEL PEAK 18(14Q21.2) MUTATED   17  0
  DEL PEAK 18(14Q21.2) WILD-TYPE 50 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(14Q21.2) MUTATED     17    0
  DEL PEAK 18(14Q21.2) WILD-TYPE   50   10
   clus
vv  DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE
  0                           17                             50
  1                            0                             10
[1] 2 2
[1] FALSE
D37V6, binary
                                cls
clus                              0  1
  DEL PEAK 18(14Q21.2) MUTATED   10  8
  DEL PEAK 18(14Q21.2) WILD-TYPE 42 20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(14Q21.2) MUTATED     10    8
  DEL PEAK 18(14Q21.2) WILD-TYPE   42   20
        clus
vv       DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE
  FEMALE                           10                             42
  MALE                              8                             20
[1] 2 2
[1] FALSE
D37V7, binary
                                cls
clus                              0  1
  DEL PEAK 18(14Q21.2) MUTATED    3  5
  DEL PEAK 18(14Q21.2) WILD-TYPE  5 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(14Q21.2) MUTATED      3    5
  DEL PEAK 18(14Q21.2) WILD-TYPE    5   22
                        clus
vv                       DEL PEAK 18(14Q21.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                            5
                        clus
vv                       DEL PEAK 18(14Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             22
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 19(16P13.3) MUTATION ANALYSIS
D38V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 19(16P13.3) MUTATED    2  4
  DEL PEAK 19(16P13.3) WILD-TYPE 50 23
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                             6                             73 
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                             4                             23 
$`DEL PEAK 19(16P13.3) MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JY TCGA-OR-A5LS TCGA-P6-A5OG 
       79.82        16.11        18.12        18.15        29.00        12.59 

$`DEL PEAK 19(16P13.3) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J8 
       44.55        55.13        63.85        15.45        12.00        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF 
       38.89        30.31        57.53        91.46        69.21        41.39 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       17.79        40.34        46.82        10.16        41.26        22.03 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       18.48        29.23         4.90        22.16       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ 
       16.04         9.50        50.66        63.25        31.23         6.94 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       33.83        89.52        32.68        93.44        17.36         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       37.15        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
       50.14        35.87        12.85         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       27.62        20.65        18.25        21.21        16.01        39.58 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH 
        5.23        39.35        21.76        14.63        52.24        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO 
       36.33        73.05        53.03        61.08        62.99        64.08 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PK-A5H9 TCGA-PK-A5HA 
       52.04        21.01        12.00        23.31        10.09        27.29 
TCGA-PK-A5HB 
       42.51 

  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                         12.59                           4.11 
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                         79.82                         153.63 
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                        18.135                         33.830 
[1] "12.6 - 79.8 (18.1)" "4.1 - 153.6 (33.8)"
[1] "hr=" "2.8"
D38V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 19(16P13.3) MUTATED         0        2         1        3
  DEL PEAK 19(16P13.3) WILD-TYPE       8       32        16       14
D38V3, multiclass
           clus
vv          DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  STAGE I                              0                              8
  STAGE II                             2                             32
  STAGE III                            1                             16
  STAGE IV                             3                             14
[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(16P13.3) MUTATED    0  2  1  3
  DEL PEAK 19(16P13.3) WILD-TYPE  8 37 10 15
D38V4, multiclass
    clus
vv   DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  T1                            0                              8
  T2                            2                             37
  T3                            1                             10
  T4                            3                             15
[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"
D38V5, binary
                                cls
clus                              0  1
  DEL PEAK 19(16P13.3) MUTATED    5  1
  DEL PEAK 19(16P13.3) WILD-TYPE 62  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(16P13.3) MUTATED      5    1
  DEL PEAK 19(16P13.3) WILD-TYPE   62    9
   clus
vv  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  0                            5                             62
  1                            1                              9
[1] 2 2
[1] FALSE
D38V6, binary
                                cls
clus                              0  1
  DEL PEAK 19(16P13.3) MUTATED    5  1
  DEL PEAK 19(16P13.3) WILD-TYPE 47 27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(16P13.3) MUTATED      5    1
  DEL PEAK 19(16P13.3) WILD-TYPE   47   27
        clus
vv       DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  FEMALE                            5                             47
  MALE                              1                             27
[1] 2 2
[1] FALSE
D38V7, binary
                                cls
clus                              0  1
  DEL PEAK 19(16P13.3) MUTATED    2  1
  DEL PEAK 19(16P13.3) WILD-TYPE  6 26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(16P13.3) MUTATED      2    1
  DEL PEAK 19(16P13.3) WILD-TYPE    6   26
                        clus
vv                       DEL PEAK 19(16P13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                            1
                        clus
vv                       DEL PEAK 19(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             26
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 20(16Q23.1) MUTATION ANALYSIS
D39V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 20(16Q23.1) MUTATED    2  4
  DEL PEAK 20(16Q23.1) WILD-TYPE 50 23
  DEL PEAK 20(16Q23.1) MUTATED DEL PEAK 20(16Q23.1) WILD-TYPE 
                             6                             73 
  DEL PEAK 20(16Q23.1) MUTATED DEL PEAK 20(16Q23.1) WILD-TYPE 
                             4                             23 
$`DEL PEAK 20(16Q23.1) MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5K0 TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LG 
       16.11        18.12        33.83        39.58        39.35        52.24 

$`DEL PEAK 20(16Q23.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       19.04        38.89        30.31        57.53        91.46        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       41.39        17.79        40.34        46.82        10.16        41.26 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       22.03        18.48        29.23         4.90        22.16       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        16.04         9.50        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
       18.15         6.94        89.52        32.68        93.44        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
        8.32        37.15        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 
      120.30        50.14        35.87        12.85         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       23.80        27.62        20.65        18.25        21.21        16.01 
TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
        5.23        21.76        14.63        78.41        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       53.03        61.08        62.99        64.08        52.04        21.01 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       29.00        12.00        23.31        12.59        10.09        27.29 
TCGA-PK-A5HB 
       42.51 

  DEL PEAK 20(16Q23.1) MUTATED DEL PEAK 20(16Q23.1) WILD-TYPE 
                         16.11                           4.11 
  DEL PEAK 20(16Q23.1) MUTATED DEL PEAK 20(16Q23.1) WILD-TYPE 
                         52.24                         153.63 
  DEL PEAK 20(16Q23.1) MUTATED DEL PEAK 20(16Q23.1) WILD-TYPE 
                         36.59                          30.31 
[1] "16.1 - 52.2 (36.6)" "4.1 - 153.6 (30.3)"
[1] "hr=" "2.5"
D39V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 20(16Q23.1) MUTATED         0        1         3        2
  DEL PEAK 20(16Q23.1) WILD-TYPE       8       33        14       15
D39V3, multiclass
           clus
vv          DEL PEAK 20(16Q23.1) MUTATED DEL PEAK 20(16Q23.1) WILD-TYPE
  STAGE I                              0                              8
  STAGE II                             1                             33
  STAGE III                            3                             14
  STAGE IV                             2                             15
[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(16Q23.1) MUTATED    0  1  2  3
  DEL PEAK 20(16Q23.1) WILD-TYPE  8 38  9 15
D39V4, multiclass
    clus
vv   DEL PEAK 20(16Q23.1) MUTATED DEL PEAK 20(16Q23.1) WILD-TYPE
  T1                            0                              8
  T2                            1                             38
  T3                            2                              9
  T4                            3                             15
[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"
D39V5, binary
                                cls
clus                              0  1
  DEL PEAK 20(16Q23.1) MUTATED    6  0
  DEL PEAK 20(16Q23.1) WILD-TYPE 61 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(16Q23.1) MUTATED      6    0
  DEL PEAK 20(16Q23.1) WILD-TYPE   61   10
   clus
vv  DEL PEAK 20(16Q23.1) MUTATED DEL PEAK 20(16Q23.1) WILD-TYPE
  0                            6                             61
  1                            0                             10
[1] 2 2
[1] FALSE
D39V6, binary
                                cls
clus                              0  1
  DEL PEAK 20(16Q23.1) MUTATED    2  4
  DEL PEAK 20(16Q23.1) WILD-TYPE 50 24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(16Q23.1) MUTATED      2    4
  DEL PEAK 20(16Q23.1) WILD-TYPE   50   24
        clus
vv       DEL PEAK 20(16Q23.1) MUTATED DEL PEAK 20(16Q23.1) WILD-TYPE
  FEMALE                            2                             50
  MALE                              4                             24
[1] 2 2
[1] FALSE
D39V7, binary
                                cls
clus                              0  1
  DEL PEAK 20(16Q23.1) MUTATED    1  3
  DEL PEAK 20(16Q23.1) WILD-TYPE  7 24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(16Q23.1) MUTATED      1    3
  DEL PEAK 20(16Q23.1) WILD-TYPE    7   24
                        clus
vv                       DEL PEAK 20(16Q23.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            3
                        clus
vv                       DEL PEAK 20(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                             24
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 21(17Q11.2) MUTATION ANALYSIS
D40V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 21(17Q11.2) MUTATED   11 12
  DEL PEAK 21(17Q11.2) WILD-TYPE 41 15
  DEL PEAK 21(17Q11.2) MUTATED DEL PEAK 21(17Q11.2) WILD-TYPE 
                            23                             56 
  DEL PEAK 21(17Q11.2) MUTATED DEL PEAK 21(17Q11.2) WILD-TYPE 
                            12                             15 
$`DEL PEAK 21(17Q11.2) MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JG TCGA-OR-A5JK 
       16.11        30.31        18.12        57.53        17.79        41.26 
TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5K9 
        4.90        12.59        50.66        63.25        32.68        11.31 
TCGA-OR-A5KY TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LM 
       12.85        20.65         5.23        39.35        21.76        61.08 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5HA TCGA-PK-A5HB 
       29.00        23.31        12.59        27.29        42.51 

$`DEL PEAK 21(17Q11.2) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JH 
       19.04        38.89        91.46        69.21        41.39        40.34 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JQ 
       46.82        10.16        22.03        18.48        29.23        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ 
      121.25        16.04         9.50        31.23        18.15         6.94 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
       33.83        89.52        93.44        17.36         8.32        37.15 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       46.49        87.88       153.63       120.30        50.14        35.87 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 
        4.11       128.12        23.80        27.62        18.25        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
       16.01        39.58        14.63        52.24        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       73.05        53.03        62.99        64.08        52.04        21.01 
TCGA-OR-A5LT TCGA-PK-A5H9 
       12.00        10.09 

  DEL PEAK 21(17Q11.2) MUTATED DEL PEAK 21(17Q11.2) WILD-TYPE 
                          4.90                           4.11 
  DEL PEAK 21(17Q11.2) MUTATED DEL PEAK 21(17Q11.2) WILD-TYPE 
                         63.25                         153.63 
  DEL PEAK 21(17Q11.2) MUTATED DEL PEAK 21(17Q11.2) WILD-TYPE 
                         23.31                          36.74 
[1] "4.9 - 63.2 (23.3)"  "4.1 - 153.6 (36.7)"
[1] "hr=" "3"  
D40V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 21(17Q11.2) MUTATED         0        9         3        8
  DEL PEAK 21(17Q11.2) WILD-TYPE       8       25        14        9
D40V3, multiclass
           clus
vv          DEL PEAK 21(17Q11.2) MUTATED DEL PEAK 21(17Q11.2) WILD-TYPE
  STAGE I                              0                              8
  STAGE II                             9                             25
  STAGE III                            3                             14
  STAGE IV                             8                              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 21(17Q11.2) MUTATED    0 10  1  9
  DEL PEAK 21(17Q11.2) WILD-TYPE  8 29 10  9
D40V4, multiclass
    clus
vv   DEL PEAK 21(17Q11.2) MUTATED DEL PEAK 21(17Q11.2) WILD-TYPE
  T1                            0                              8
  T2                           10                             29
  T3                            1                             10
  T4                            9                              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"
D40V5, binary
                                cls
clus                              0  1
  DEL PEAK 21(17Q11.2) MUTATED   18  3
  DEL PEAK 21(17Q11.2) WILD-TYPE 49  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(17Q11.2) MUTATED     18    3
  DEL PEAK 21(17Q11.2) WILD-TYPE   49    7
   clus
vv  DEL PEAK 21(17Q11.2) MUTATED DEL PEAK 21(17Q11.2) WILD-TYPE
  0                           18                             49
  1                            3                              7
[1] 2 2
[1] FALSE
D40V6, binary
                                cls
clus                              0  1
  DEL PEAK 21(17Q11.2) MUTATED   10 13
  DEL PEAK 21(17Q11.2) WILD-TYPE 42 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(17Q11.2) MUTATED     10   13
  DEL PEAK 21(17Q11.2) WILD-TYPE   42   15
        clus
vv       DEL PEAK 21(17Q11.2) MUTATED DEL PEAK 21(17Q11.2) WILD-TYPE
  FEMALE                           10                             42
  MALE                             13                             15
[1] 2 2
[1] FALSE
D40V7, binary
                                cls
clus                              0  1
  DEL PEAK 21(17Q11.2) MUTATED    1  7
  DEL PEAK 21(17Q11.2) WILD-TYPE  7 20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(17Q11.2) MUTATED      1    7
  DEL PEAK 21(17Q11.2) WILD-TYPE    7   20
                        clus
vv                       DEL PEAK 21(17Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            7
                        clus
vv                       DEL PEAK 21(17Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                             20
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 22(17Q21.31) MUTATION ANALYSIS
D41V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 22(17Q21.31) MUTATED   14 11
  DEL PEAK 22(17Q21.31) WILD-TYPE 38 16
  DEL PEAK 22(17Q21.31) MUTATED DEL PEAK 22(17Q21.31) WILD-TYPE 
                             25                              54 
  DEL PEAK 22(17Q21.31) MUTATED DEL PEAK 22(17Q21.31) WILD-TYPE 
                             11                              16 
$`DEL PEAK 22(17Q21.31) MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JG TCGA-OR-A5JK TCGA-OR-A5JP 
       16.11        30.31        57.53        17.79        41.26         4.90 
TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5K9 TCGA-OR-A5KT 
       12.59        50.66        63.25        32.68        11.31        87.88 
TCGA-OR-A5KY TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG 
       12.85        20.65         5.23        39.35        21.76        52.24 
TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5HA 
       61.08        64.08        29.00        23.31        12.59        27.29 
TCGA-PK-A5HB 
       42.51 

$`DEL PEAK 22(17Q21.31) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        38.89        18.12        91.46        69.21        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       40.34        46.82        10.16        22.03        18.48        29.23 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JX TCGA-OR-A5JY 
       22.16       121.25        16.04         9.50        31.23        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
        6.94        33.83        89.52        93.44        17.36         8.32 
TCGA-OR-A5K6 TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       37.15        46.49       153.63       120.30        50.14        35.87 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 
        4.11       128.12        23.80        27.62        18.25        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       16.01        39.58        14.63        78.41        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-PK-A5H9 
       53.03        62.99        52.04        21.01        12.00        10.09 

  DEL PEAK 22(17Q21.31) MUTATED DEL PEAK 22(17Q21.31) WILD-TYPE 
                           4.90                            4.11 
  DEL PEAK 22(17Q21.31) MUTATED DEL PEAK 22(17Q21.31) WILD-TYPE 
                          87.88                          153.63 
  DEL PEAK 22(17Q21.31) MUTATED DEL PEAK 22(17Q21.31) WILD-TYPE 
                          29.00                           34.85 
[1] "4.9 - 87.9 (29.0)"  "4.1 - 153.6 (34.8)"
[1] "hr=" "1.8"
D41V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 22(17Q21.31) MUTATED         1       10         4        8
  DEL PEAK 22(17Q21.31) WILD-TYPE       7       24        13        9
D41V3, multiclass
           clus
vv          DEL PEAK 22(17Q21.31) MUTATED DEL PEAK 22(17Q21.31) WILD-TYPE
  STAGE I                               1                               7
  STAGE II                             10                              24
  STAGE III                             4                              13
  STAGE IV                              8                               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 22(17Q21.31) MUTATED    1 11  2  9
  DEL PEAK 22(17Q21.31) WILD-TYPE  7 28  9  9
D41V4, multiclass
    clus
vv   DEL PEAK 22(17Q21.31) MUTATED DEL PEAK 22(17Q21.31) WILD-TYPE
  T1                             1                               7
  T2                            11                              28
  T3                             2                               9
  T4                             9                               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"
D41V5, binary
                                 cls
clus                               0  1
  DEL PEAK 22(17Q21.31) MUTATED   21  3
  DEL PEAK 22(17Q21.31) WILD-TYPE 46  7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(17Q21.31) MUTATED     21    3
  DEL PEAK 22(17Q21.31) WILD-TYPE   46    7
   clus
vv  DEL PEAK 22(17Q21.31) MUTATED DEL PEAK 22(17Q21.31) WILD-TYPE
  0                            21                              46
  1                             3                               7
[1] 2 2
[1] FALSE
D41V6, binary
                                 cls
clus                               0  1
  DEL PEAK 22(17Q21.31) MUTATED   13 13
  DEL PEAK 22(17Q21.31) WILD-TYPE 39 15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(17Q21.31) MUTATED     13   13
  DEL PEAK 22(17Q21.31) WILD-TYPE   39   15
        clus
vv       DEL PEAK 22(17Q21.31) MUTATED DEL PEAK 22(17Q21.31) WILD-TYPE
  FEMALE                            13                              39
  MALE                              13                              15
[1] 2 2
[1] FALSE
D41V7, binary
                                 cls
clus                               0  1
  DEL PEAK 22(17Q21.31) MUTATED    1 10
  DEL PEAK 22(17Q21.31) WILD-TYPE  7 17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(17Q21.31) MUTATED      1   10
  DEL PEAK 22(17Q21.31) WILD-TYPE    7   17
                        clus
vv                       DEL PEAK 22(17Q21.31) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            10
                        clus
vv                       DEL PEAK 22(17Q21.31) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                              17
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 23(17Q24.2) MUTATION ANALYSIS
D42V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 23(17Q24.2) MUTATED   12 12
  DEL PEAK 23(17Q24.2) WILD-TYPE 40 15
  DEL PEAK 23(17Q24.2) MUTATED DEL PEAK 23(17Q24.2) WILD-TYPE 
                            24                             55 
  DEL PEAK 23(17Q24.2) MUTATED DEL PEAK 23(17Q24.2) WILD-TYPE 
                            12                             15 
$`DEL PEAK 23(17Q24.2) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JG TCGA-OR-A5JK 
       15.45        16.11        30.31        57.53        17.79        41.26 
TCGA-OR-A5JM TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5K6 TCGA-OR-A5K9 
       18.48        12.59        50.66        63.25        37.15        11.31 
TCGA-OR-A5KY TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG 
       12.85        20.65        39.58         5.23        21.76        52.24 
TCGA-OR-A5LM TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5HA TCGA-PK-A5HB 
       61.08        29.00        23.31        12.59        27.29        42.51 

$`DEL PEAK 23(17Q24.2) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 
       44.55        55.13        63.85        12.00        79.82        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JH 
       38.89        18.12        91.46        69.21        41.39        40.34 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       46.82        10.16        22.03        29.23         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ 
      121.25        16.04         9.50        31.23        18.15         6.94 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       33.83        89.52        32.68        93.44        17.36         8.32 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       46.49        87.88       153.63       120.30        50.14        35.87 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 
        4.11       128.12        23.80        27.62        18.25        21.21 
TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       16.01        39.35        14.63        78.41        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT 
       53.03        62.99        64.08        52.04        21.01        12.00 
TCGA-PK-A5H9 
       10.09 

  DEL PEAK 23(17Q24.2) MUTATED DEL PEAK 23(17Q24.2) WILD-TYPE 
                          5.23                           4.11 
  DEL PEAK 23(17Q24.2) MUTATED DEL PEAK 23(17Q24.2) WILD-TYPE 
                         63.25                         153.63 
  DEL PEAK 23(17Q24.2) MUTATED DEL PEAK 23(17Q24.2) WILD-TYPE 
                         25.30                          35.87 
[1] "5.2 - 63.2 (25.3)"  "4.1 - 153.6 (35.9)"
[1] "hr=" "2.6"
D42V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 23(17Q24.2) MUTATED         0        9         2       10
  DEL PEAK 23(17Q24.2) WILD-TYPE       8       25        15        7
D42V3, multiclass
           clus
vv          DEL PEAK 23(17Q24.2) MUTATED DEL PEAK 23(17Q24.2) WILD-TYPE
  STAGE I                              0                              8
  STAGE II                             9                             25
  STAGE III                            2                             15
  STAGE IV                            10                              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 23(17Q24.2) MUTATED    0 10  3  8
  DEL PEAK 23(17Q24.2) WILD-TYPE  8 29  8 10
D42V4, multiclass
    clus
vv   DEL PEAK 23(17Q24.2) MUTATED DEL PEAK 23(17Q24.2) WILD-TYPE
  T1                            0                              8
  T2                           10                             29
  T3                            3                              8
  T4                            8                             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"
D42V5, binary
                                cls
clus                              0  1
  DEL PEAK 23(17Q24.2) MUTATED   18  4
  DEL PEAK 23(17Q24.2) WILD-TYPE 49  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(17Q24.2) MUTATED     18    4
  DEL PEAK 23(17Q24.2) WILD-TYPE   49    6
   clus
vv  DEL PEAK 23(17Q24.2) MUTATED DEL PEAK 23(17Q24.2) WILD-TYPE
  0                           18                             49
  1                            4                              6
[1] 2 2
[1] FALSE
D42V6, binary
                                cls
clus                              0  1
  DEL PEAK 23(17Q24.2) MUTATED   12 12
  DEL PEAK 23(17Q24.2) WILD-TYPE 40 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(17Q24.2) MUTATED     12   12
  DEL PEAK 23(17Q24.2) WILD-TYPE   40   16
        clus
vv       DEL PEAK 23(17Q24.2) MUTATED DEL PEAK 23(17Q24.2) WILD-TYPE
  FEMALE                           12                             40
  MALE                             12                             16
[1] 2 2
[1] FALSE
D42V7, binary
                                cls
clus                              0  1
  DEL PEAK 23(17Q24.2) MUTATED    2  9
  DEL PEAK 23(17Q24.2) WILD-TYPE  6 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(17Q24.2) MUTATED      2    9
  DEL PEAK 23(17Q24.2) WILD-TYPE    6   18
                        clus
vv                       DEL PEAK 23(17Q24.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                            9
                        clus
vv                       DEL PEAK 23(17Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             18
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 24(18Q21.2) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 24(18Q21.2) MUTATED   22 11
  DEL PEAK 24(18Q21.2) WILD-TYPE 30 16
  DEL PEAK 24(18Q21.2) MUTATED DEL PEAK 24(18Q21.2) WILD-TYPE 
                            33                             46 
  DEL PEAK 24(18Q21.2) MUTATED DEL PEAK 24(18Q21.2) WILD-TYPE 
                            11                             16 
$`DEL PEAK 24(18Q21.2) MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG 
       79.82        16.11        18.12        57.53        91.46        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JP 
       40.34        46.82        41.26        22.03        18.48         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       22.16        12.59        16.04        50.66        63.25        31.23 
TCGA-OR-A5K2 TCGA-OR-A5KY TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG 
       32.68        12.85        20.65         5.23        21.76        52.24 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       53.03        61.08        62.99        29.00        12.00        23.31 
TCGA-P6-A5OG TCGA-PK-A5HA TCGA-PK-A5HB 
       12.59        27.29        42.51 

$`DEL PEAK 24(18Q21.2) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J8 
       44.55        55.13        63.85        15.45        12.00        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JO 
       38.89        30.31        69.21        41.39        10.16        29.23 
TCGA-OR-A5JR TCGA-OR-A5JU TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
      121.25         9.50        18.15         6.94        33.83        89.52 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO 
       93.44        17.36         8.32        37.15        11.31        46.49 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       87.88       153.63       120.30        50.14        35.87         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      128.12        23.80        27.62        18.25        21.21        16.01 
TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       39.58        39.35        14.63        78.41        36.33        73.05 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PK-A5H9 
       64.08        52.04        21.01        10.09 

  DEL PEAK 24(18Q21.2) MUTATED DEL PEAK 24(18Q21.2) WILD-TYPE 
                          4.90                           4.11 
  DEL PEAK 24(18Q21.2) MUTATED DEL PEAK 24(18Q21.2) WILD-TYPE 
                         91.46                         153.63 
  DEL PEAK 24(18Q21.2) MUTATED DEL PEAK 24(18Q21.2) WILD-TYPE 
                         27.29                          36.10 
[1] "4.9 - 91.5 (27.3)"  "4.1 - 153.6 (36.1)"
[1] "hr=" "1.1"
D43V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 24(18Q21.2) MUTATED         2       15         5        9
  DEL PEAK 24(18Q21.2) WILD-TYPE       6       19        12        8
D43V3, multiclass
           clus
vv          DEL PEAK 24(18Q21.2) MUTATED DEL PEAK 24(18Q21.2) WILD-TYPE
  STAGE I                              2                              6
  STAGE II                            15                             19
  STAGE III                            5                             12
  STAGE IV                             9                              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 24(18Q21.2) MUTATED    2 16  4  9
  DEL PEAK 24(18Q21.2) WILD-TYPE  6 23  7  9
D43V4, multiclass
    clus
vv   DEL PEAK 24(18Q21.2) MUTATED DEL PEAK 24(18Q21.2) WILD-TYPE
  T1                            2                              6
  T2                           16                             23
  T3                            4                              7
  T4                            9                              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"
D43V5, binary
                                cls
clus                              0  1
  DEL PEAK 24(18Q21.2) MUTATED   29  3
  DEL PEAK 24(18Q21.2) WILD-TYPE 38  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(18Q21.2) MUTATED     29    3
  DEL PEAK 24(18Q21.2) WILD-TYPE   38    7
   clus
vv  DEL PEAK 24(18Q21.2) MUTATED DEL PEAK 24(18Q21.2) WILD-TYPE
  0                           29                             38
  1                            3                              7
[1] 2 2
[1] FALSE
D43V6, binary
                                cls
clus                              0  1
  DEL PEAK 24(18Q21.2) MUTATED   18 16
  DEL PEAK 24(18Q21.2) WILD-TYPE 34 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(18Q21.2) MUTATED     18   16
  DEL PEAK 24(18Q21.2) WILD-TYPE   34   12
        clus
vv       DEL PEAK 24(18Q21.2) MUTATED DEL PEAK 24(18Q21.2) WILD-TYPE
  FEMALE                           18                             34
  MALE                             16                             12
[1] 2 2
[1] FALSE
D43V7, binary
                                cls
clus                              0  1
  DEL PEAK 24(18Q21.2) MUTATED    2  8
  DEL PEAK 24(18Q21.2) WILD-TYPE  6 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(18Q21.2) MUTATED      2    8
  DEL PEAK 24(18Q21.2) WILD-TYPE    6   19
                        clus
vv                       DEL PEAK 24(18Q21.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                            8
                        clus
vv                       DEL PEAK 24(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             19
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 25(20P12.1) MUTATION ANALYSIS
D44V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 25(20P12.1) MUTATED    3  6
  DEL PEAK 25(20P12.1) WILD-TYPE 49 21
  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                             9                             70 
  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                             6                             21 
$`DEL PEAK 25(20P12.1) MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5JS 
       55.13        16.11        30.31        18.12        18.48        12.59 
TCGA-OR-A5K0 TCGA-OR-A5K9 TCGA-PK-A5HB 
       33.83        11.31        42.51 

$`DEL PEAK 25(20P12.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 
       44.55        63.85        15.45        12.00        79.82        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       38.89        57.53        91.46        69.21        41.39        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JO 
       40.34        46.82        10.16        41.26        22.03        29.23 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
        4.90        22.16       121.25        16.04         9.50        50.66 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 
       63.25        31.23        18.15         6.94        89.52        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5KO TCGA-OR-A5KT 
       93.44        17.36         8.32        37.15        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       120.30        50.14        35.87        12.85         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      128.12        23.80        27.62        20.65        18.25        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       16.01        39.58         5.23        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       52.24        78.41        36.33        73.05        53.03        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       62.99        64.08        52.04        21.01        29.00        12.00 
TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       23.31        12.59        10.09        27.29 

  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                         11.31                           4.11 
  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                         55.13                         153.63 
  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                        18.480                         34.275 
[1] "11.3 - 55.1 (18.5)" "4.1 - 153.6 (34.3)"
[1] "hr=" "3.4"
D44V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 25(20P12.1) MUTATED         0        3         1        4
  DEL PEAK 25(20P12.1) WILD-TYPE       8       31        16       13
D44V3, multiclass
           clus
vv          DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE
  STAGE I                              0                              8
  STAGE II                             3                             31
  STAGE III                            1                             16
  STAGE IV                             4                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 25(20P12.1) MUTATED    0  3  2  3
  DEL PEAK 25(20P12.1) WILD-TYPE  8 36  9 15
D44V4, multiclass
    clus
vv   DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE
  T1                            0                              8
  T2                            3                             36
  T3                            2                              9
  T4                            3                             15
[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"
D44V5, binary
                                cls
clus                              0  1
  DEL PEAK 25(20P12.1) MUTATED    8  0
  DEL PEAK 25(20P12.1) WILD-TYPE 59 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(20P12.1) MUTATED      8    0
  DEL PEAK 25(20P12.1) WILD-TYPE   59   10
   clus
vv  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE
  0                            8                             59
  1                            0                             10
[1] 2 2
[1] FALSE
D44V6, binary
                                cls
clus                              0  1
  DEL PEAK 25(20P12.1) MUTATED    7  2
  DEL PEAK 25(20P12.1) WILD-TYPE 45 26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(20P12.1) MUTATED      7    2
  DEL PEAK 25(20P12.1) WILD-TYPE   45   26
        clus
vv       DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE
  FEMALE                            7                             45
  MALE                              2                             26
[1] 2 2
[1] FALSE
D44V7, binary
                                cls
clus                              0  1
  DEL PEAK 25(20P12.1) MUTATED    2  0
  DEL PEAK 25(20P12.1) WILD-TYPE  6 27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(20P12.1) MUTATED      2    0
  DEL PEAK 25(20P12.1) WILD-TYPE    6   27
                        clus
vv                       DEL PEAK 25(20P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                            0
                        clus
vv                       DEL PEAK 25(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             27
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 26(22Q12.1) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 26(22Q12.1) MUTATED   26 19
  DEL PEAK 26(22Q12.1) WILD-TYPE 26  8
  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE 
                            45                             34 
  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE 
                            19                              8 
$`DEL PEAK 26(22Q12.1) MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 
       55.13        63.85        79.82        16.11        19.04        38.89 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JG 
       30.31        18.12        57.53        91.46        69.21        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       40.34        46.82        41.26         4.90        22.16       121.25 
TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
        9.50        50.66        63.25        31.23        18.15        32.68 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
        8.32        11.31        46.49        35.87        12.85         4.11 
TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LL 
       20.65        39.58         5.23        21.76        52.24        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       61.08        62.99        64.08        29.00        12.00        23.31 
TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       12.59        10.09        27.29 

$`DEL PEAK 26(22Q12.1) WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL 
       44.55        15.45        12.00        41.39        10.16        22.03 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JZ TCGA-OR-A5K0 
       18.48        29.23        12.59        16.04         6.94        33.83 
TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5KT TCGA-OR-A5KU 
       89.52        93.44        17.36        37.15        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 
      120.30        50.14       128.12        23.80        27.62        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ 
       21.21        16.01        39.35        14.63        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PK-A5HB 
       73.05        52.04        21.01        42.51 

  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE 
                          4.11                           6.94 
  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE 
                        121.25                         153.63 
  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE 
                         31.23                          31.53 
[1] "4.1 - 121.2 (31.2)" "6.9 - 153.6 (31.5)"
[1] "hr=" "2"  
D45V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 26(22Q12.1) MUTATED         3       17        10       13
  DEL PEAK 26(22Q12.1) WILD-TYPE       5       17         7        4
D45V3, multiclass
           clus
vv          DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE
  STAGE I                              3                              5
  STAGE II                            17                             17
  STAGE III                           10                              7
  STAGE IV                            13                              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
  DEL PEAK 26(22Q12.1) MUTATED    3 19  9 12
  DEL PEAK 26(22Q12.1) WILD-TYPE  5 20  2  6
D45V4, multiclass
    clus
vv   DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE
  T1                            3                              5
  T2                           19                             20
  T3                            9                              2
  T4                           12                              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"
D45V5, binary
                                cls
clus                              0  1
  DEL PEAK 26(22Q12.1) MUTATED   39  5
  DEL PEAK 26(22Q12.1) WILD-TYPE 28  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(22Q12.1) MUTATED     39    5
  DEL PEAK 26(22Q12.1) WILD-TYPE   28    5
   clus
vv  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE
  0                           39                             28
  1                            5                              5
[1] 2 2
[1] FALSE
D45V6, binary
                                cls
clus                              0  1
  DEL PEAK 26(22Q12.1) MUTATED   27 19
  DEL PEAK 26(22Q12.1) WILD-TYPE 25  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(22Q12.1) MUTATED     27   19
  DEL PEAK 26(22Q12.1) WILD-TYPE   25    9
        clus
vv       DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE
  FEMALE                           27                             25
  MALE                             19                              9
[1] 2 2
[1] FALSE
D45V7, binary
                                cls
clus                              0  1
  DEL PEAK 26(22Q12.1) MUTATED    6 13
  DEL PEAK 26(22Q12.1) WILD-TYPE  2 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(22Q12.1) MUTATED      6   13
  DEL PEAK 26(22Q12.1) WILD-TYPE    2   14
                        clus
vv                       DEL PEAK 26(22Q12.1) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           13
                        clus
vv                       DEL PEAK 26(22Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             14
[1] 2 2
[1] FALSE
