[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/22489368/ACC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ACC-TP/22522857/transformed.cor.cli.txt"

nPatients in clinical file=92, in cluster file=90, common to both=90
[1] 44 90
[1] "AMP PEAK  1(1Q22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         17                          73 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         17                          73 
[1] "AMP PEAK  2(4P16.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                           41                            49 
  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                           41                            49 
[1] "AMP PEAK  3(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(5P15.33) MUTATED AMP PEAK  3(5P15.33) WILD-TYPE 
                            65                             25 
  AMP PEAK  3(5P15.33) MUTATED AMP PEAK  3(5P15.33) WILD-TYPE 
                            65                             25 
[1] "AMP PEAK  4(5Q35.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(5Q35.3) MUTATED AMP PEAK  4(5Q35.3) WILD-TYPE 
                           63                            27 
  AMP PEAK  4(5Q35.3) MUTATED AMP PEAK  4(5Q35.3) WILD-TYPE 
                           63                            27 
[1] "AMP PEAK  5(6P21.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(6P21.31) MUTATED AMP PEAK  5(6P21.31) WILD-TYPE 
                            19                             71 
  AMP PEAK  5(6P21.31) MUTATED AMP PEAK  5(6P21.31) WILD-TYPE 
                            19                             71 
[1] "AMP PEAK  6(6Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE 
                           19                            71 
  AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE 
                           19                            71 
[1] "AMP PEAK  7(7P22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(7P22.1) MUTATED AMP PEAK  7(7P22.1) WILD-TYPE 
                           54                            36 
  AMP PEAK  7(7P22.1) MUTATED AMP PEAK  7(7P22.1) WILD-TYPE 
                           54                            36 
[1] "AMP PEAK  8(9Q31.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(9Q31.3) MUTATED AMP PEAK  8(9Q31.3) WILD-TYPE 
                           34                            56 
  AMP PEAK  8(9Q31.3) MUTATED AMP PEAK  8(9Q31.3) WILD-TYPE 
                           34                            56 
[1] "AMP PEAK  9(12Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE 
                            70                             20 
  AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE 
                            70                             20 
[1] "AMP PEAK 10(14Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(14Q11.2) MUTATED AMP PEAK 10(14Q11.2) WILD-TYPE 
                            27                             63 
  AMP PEAK 10(14Q11.2) MUTATED AMP PEAK 10(14Q11.2) WILD-TYPE 
                            27                             63 
[1] "AMP PEAK 11(16P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(16P13.3) MUTATED AMP PEAK 11(16P13.3) WILD-TYPE 
                            50                             40 
  AMP PEAK 11(16P13.3) MUTATED AMP PEAK 11(16P13.3) WILD-TYPE 
                            50                             40 
[1] "AMP PEAK 12(16Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(16Q22.1) MUTATED AMP PEAK 12(16Q22.1) WILD-TYPE 
                            56                             34 
  AMP PEAK 12(16Q22.1) MUTATED AMP PEAK 12(16Q22.1) WILD-TYPE 
                            56                             34 
[1] "AMP PEAK 13(16Q24.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(16Q24.2) MUTATED AMP PEAK 13(16Q24.2) WILD-TYPE 
                            49                             41 
  AMP PEAK 13(16Q24.2) MUTATED AMP PEAK 13(16Q24.2) WILD-TYPE 
                            49                             41 
[1] "AMP PEAK 14(17Q25.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(17Q25.3) MUTATED AMP PEAK 14(17Q25.3) WILD-TYPE 
                            18                             72 
  AMP PEAK 14(17Q25.3) MUTATED AMP PEAK 14(17Q25.3) WILD-TYPE 
                            18                             72 
[1] "AMP PEAK 15(19P13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(19P13.12) MUTATED AMP PEAK 15(19P13.12) WILD-TYPE 
                             58                              32 
  AMP PEAK 15(19P13.12) MUTATED AMP PEAK 15(19P13.12) WILD-TYPE 
                             58                              32 
[1] "AMP PEAK 16(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(19Q12) MUTATED AMP PEAK 16(19Q12) WILD-TYPE 
                          56                           34 
  AMP PEAK 16(19Q12) MUTATED AMP PEAK 16(19Q12) WILD-TYPE 
                          56                           34 
[1] "AMP PEAK 17(XP11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(XP11.22) MUTATED AMP PEAK 17(XP11.22) WILD-TYPE 
                            49                             41 
  AMP PEAK 17(XP11.22) MUTATED AMP PEAK 17(XP11.22) WILD-TYPE 
                            49                             41 
[1] "AMP PEAK 18(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(XQ28) MUTATED AMP PEAK 18(XQ28) WILD-TYPE 
                         46                          44 
  AMP PEAK 18(XQ28) MUTATED AMP PEAK 18(XQ28) WILD-TYPE 
                         46                          44 
[1] "DEL PEAK  1(1P36.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            38                             52 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            38                             52 
[1] "DEL PEAK  2(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                           18                            72 
  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                           18                            72 
[1] "DEL PEAK  3(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           21                            69 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           21                            69 
[1] "DEL PEAK  4(3Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(3Q13.31) MUTATED DEL PEAK  4(3Q13.31) WILD-TYPE 
                            25                             65 
  DEL PEAK  4(3Q13.31) MUTATED DEL PEAK  4(3Q13.31) WILD-TYPE 
                            25                             65 
[1] "DEL PEAK  5(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                           25                            65 
  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                           25                            65 
[1] "DEL PEAK  6(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           28                            62 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           28                            62 
[1] "DEL PEAK  7(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                           30                            60 
  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                           30                            60 
[1] "DEL PEAK  8(6P24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE 
                           20                            70 
  DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE 
                           20                            70 
[1] "DEL PEAK  9(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                         21                          69 
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                         21                          69 
[1] "DEL PEAK 10(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(7Q36.3) MUTATED DEL PEAK 10(7Q36.3) WILD-TYPE 
                           11                            79 
  DEL PEAK 10(7Q36.3) MUTATED DEL PEAK 10(7Q36.3) WILD-TYPE 
                           11                            79 
[1] "DEL PEAK 11(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE 
                         23                          67 
  DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE 
                         23                          67 
[1] "DEL PEAK 12(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           26                            64 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           26                            64 
[1] "DEL PEAK 13(10Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE 
                            10                             80 
  DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE 
                            10                             80 
[1] "DEL PEAK 14(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                            26                             64 
  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                            26                             64 
[1] "DEL PEAK 15(11Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                            24                             66 
  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                            24                             66 
[1] "DEL PEAK 16(12Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE 
                             5                             85 
  DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE 
                             5                             85 
[1] "DEL PEAK 17(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                            42                             48 
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                            42                             48 
[1] "DEL PEAK 18(14Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE 
                            20                             70 
  DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE 
                            20                             70 
[1] "DEL PEAK 19(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(15Q15.1) MUTATED DEL PEAK 19(15Q15.1) WILD-TYPE 
                            25                             65 
  DEL PEAK 19(15Q15.1) MUTATED DEL PEAK 19(15Q15.1) WILD-TYPE 
                            25                             65 
[1] "DEL PEAK 20(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE 
                             8                             82 
  DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE 
                             8                             82 
[1] "DEL PEAK 21(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                            11                             79 
  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                            11                             79 
[1] "DEL PEAK 22(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(17Q11.2) MUTATED DEL PEAK 22(17Q11.2) WILD-TYPE 
                            24                             66 
  DEL PEAK 22(17Q11.2) MUTATED DEL PEAK 22(17Q11.2) WILD-TYPE 
                            24                             66 
[1] "DEL PEAK 23(17Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(17Q21.2) MUTATED DEL PEAK 23(17Q21.2) WILD-TYPE 
                            26                             64 
  DEL PEAK 23(17Q21.2) MUTATED DEL PEAK 23(17Q21.2) WILD-TYPE 
                            26                             64 
[1] "DEL PEAK 24(17Q24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(17Q24.2) MUTATED DEL PEAK 24(17Q24.2) WILD-TYPE 
                            24                             66 
  DEL PEAK 24(17Q24.2) MUTATED DEL PEAK 24(17Q24.2) WILD-TYPE 
                            24                             66 
[1] "DEL PEAK 25(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                            12                             78 
  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                            12                             78 
[1] "DEL PEAK 26(22Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE 
                            50                             40 
  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE 
                            50                             40 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RESIDUAL_TUMOR"                      
[15] "NUMBER_OF_LYMPH_NODES"               
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 90 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=32,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 90 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"        "PATHOLOGIC_STAGE"      "PATHOLOGY_T_STAGE"    
 [4] "PATHOLOGY_N_STAGE"     "GENDER"                "RADIATION_THERAPY"    
 [7] "HISTOLOGICAL_TYPE"     "RESIDUAL_TUMOR"        "NUMBER_OF_LYMPH_NODES"
[10] "RACE"                  "ETHNICITY"            
YEARS_TO_BIRTH, nv=50, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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 
 9 48 11 20 
[1] "table(vv)"
vv
T1 T2 T3 T4 
 9 48 11 20 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 T4 
 9 48 11 20 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
 9 48 11 20 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=7, binary=FALSE, numeric=TRUE
RACE, nv=3, 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    6 11
  AMP PEAK  1(1Q22) WILD-TYPE 51 22
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         17                          73 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         11                          22 
$`AMP PEAK  1(1Q22) MUTATED`
TCGA-OR-A5K0 TCGA-P6-A5OG TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J7 TCGA-OR-A5JB 
       33.83        12.59        44.55        55.13        16.11        18.12 
TCGA-OR-A5JE TCGA-OR-A5JK TCGA-OR-A5JV TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KB 
       69.21        49.22        66.51        16.37        11.31        24.36 
TCGA-OR-A5KX TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LL TCGA-PK-A5HC 
       44.84         5.23        21.76        53.03        22.32 

$`AMP PEAK  1(1Q22) WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J3 TCGA-OR-A5J4 
       91.30        43.30        39.58        42.51        68.75        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC 
       12.00        88.87        19.04        44.45        30.31        57.53 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       99.88        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       67.59        18.48        39.25        15.25        36.26       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       12.59        29.82         9.50        72.39        31.23        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 
       27.02       108.13        32.68       113.92        35.57        49.08 
TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       24.62        46.49        88.01        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        68.25        12.85         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        28.31        29.10        28.64        23.64 
TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ 
       39.35        14.63        52.24        78.41        14.33        36.33 
TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       90.08        61.08        77.00        79.07        61.05        28.04 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 
       36.03        18.05        38.50         0.00        24.85        20.25 
TCGA-PK-A5HA 
       39.48 

  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                       5.23                        0.00 
  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 
                      24.36                       39.35 
[1] "5.2 - 69.2 (24.4)"  "0.0 - 153.6 (39.4)"
[1] "hr=" "3"  
D1V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  1(1Q22) MUTATED         1        7         4        5
  AMP PEAK  1(1Q22) WILD-TYPE       8       36        14       13
D1V3, multiclass
           clus
vv          AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  STAGE I                           1                           8
  STAGE II                          7                          36
  STAGE III                         4                          14
  STAGE IV                          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"
                             vv
clus                          T1 T2 T3 T4
  AMP PEAK  1(1Q22) MUTATED    1  8  3  5
  AMP PEAK  1(1Q22) WILD-TYPE  8 40  8 15
D1V4, multiclass
    clus
vv   AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  T1                         1                           8
  T2                         8                          40
  T3                         3                           8
  T4                         5                          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"
D1V5, binary
                             cls
clus                           0  1
  AMP PEAK  1(1Q22) MUTATED   16  1
  AMP PEAK  1(1Q22) WILD-TYPE 62  9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q22) MUTATED     16    1
  AMP PEAK  1(1Q22) WILD-TYPE   62    9
   clus
vv  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  0                        16                          62
  1                         1                           9
[1] 2 2
[1] FALSE
D1V6, binary
                             cls
clus                           0  1
  AMP PEAK  1(1Q22) MUTATED   12  5
  AMP PEAK  1(1Q22) WILD-TYPE 47 26
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q22) MUTATED     12    5
  AMP PEAK  1(1Q22) WILD-TYPE   47   26
        clus
vv       AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  FEMALE                        12                          47
  MALE                           5                          26
[1] 2 2
[1] FALSE
D1V7, binary
                             cls
clus                           0  1
  AMP PEAK  1(1Q22) MUTATED   14  2
  AMP PEAK  1(1Q22) WILD-TYPE 55 16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q22) MUTATED     14    2
  AMP PEAK  1(1Q22) WILD-TYPE   55   16
     clus
vv    AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  NO                         14                          55
  YES                         2                          16
[1] 2 2
[1] FALSE
                             vv
clus                          ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AMP PEAK  1(1Q22) MUTATED                                       0
  AMP PEAK  1(1Q22) WILD-TYPE                                     1
                             vv
clus                          ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AMP PEAK  1(1Q22) MUTATED                                          0
  AMP PEAK  1(1Q22) WILD-TYPE                                        4
                             vv
clus                          ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AMP PEAK  1(1Q22) MUTATED                                     17
  AMP PEAK  1(1Q22) WILD-TYPE                                   68
D1V8, multiclass
                                          clus
vv                                         AMP PEAK  1(1Q22) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                            0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                         0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                            17
                                          clus
vv                                         AMP PEAK  1(1Q22) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                           4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                              68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          R0 R1 R2 RX
  AMP PEAK  1(1Q22) MUTATED   10  3  4  0
  AMP PEAK  1(1Q22) WILD-TYPE 53  4  8  5
D1V9, multiclass
    clus
vv   AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  R0                        10                          53
  R1                         3                           4
  R2                         4                           8
  RX                         0                           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"
D1V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1Q22) MUTATED       1                         0    15
  AMP PEAK  1(1Q22) WILD-TYPE     1                         1    61
D1V11, multiclass
                           clus
vv                          AMP PEAK  1(1Q22) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            15
                           clus
vv                          AMP PEAK  1(1Q22) WILD-TYPE
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
                             cls
clus                           0  1
  AMP PEAK  1(1Q22) MUTATED    2  6
  AMP PEAK  1(1Q22) WILD-TYPE  6 32
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q22) MUTATED      2    6
  AMP PEAK  1(1Q22) WILD-TYPE    6   32
                        clus
vv                       AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE
  HISPANIC OR LATINO                             2                           6
  NOT HISPANIC OR LATINO                         6                          32
[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   29 12
  AMP PEAK  2(4P16.3) WILD-TYPE 28 21
  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                           41                            49 
  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                           12                            21 
$`AMP PEAK  2(4P16.3) MUTATED`
TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J9 
       39.58        44.55        13.91        12.00        16.11        44.45 
TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       30.31        57.53        66.25        69.37        76.64        16.11 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        67.59        15.25        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KB 
       66.51       113.92        35.57        16.37        24.62        24.36 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5L1 
       46.49        83.80        95.18       153.63        68.25        58.55 
TCGA-OR-A5LA TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       23.64        14.63        78.41        90.08        53.03        61.08 
TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PK-A5HC 
       77.00        36.03        18.05        38.50        22.32 

$`AMP PEAK  2(4P16.3) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J2 
       33.83        91.30        43.30        12.59        42.51        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE 
       68.75        88.87        19.04        18.12        99.88        69.21 
TCGA-OR-A5JG TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW 
       17.79        18.48        39.25        12.59         9.50        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K6 
       31.23        18.15        27.02       108.13        32.68        49.08 
TCGA-OR-A5K9 TCGA-OR-A5KQ TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
       11.31        88.01       127.50        44.84        12.85         4.11 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
       60.89       152.15        31.79        28.31        29.10        28.64 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LJ 
        5.23        39.35        21.76        52.24        14.33        36.33 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 
       79.07        61.05        28.04         0.00        24.85        20.25 
TCGA-PK-A5HA 
       39.48 

  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                           12                             0 
  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                       153.63                        152.15 
  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE 
                        44.55                         32.68 
[1] "12.0 - 153.6 (44.5)" "0.0 - 152.2 (32.7)" 
[1] "hr=" "1.7"
D2V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  2(4P16.3) MUTATED         4       21         8        7
  AMP PEAK  2(4P16.3) WILD-TYPE       5       22        10       11
D2V3, multiclass
           clus
vv          AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE
  STAGE I                             4                             5
  STAGE II                           21                            22
  STAGE III                           8                            10
  STAGE IV                            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"
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK  2(4P16.3) MUTATED    4 23  5  8
  AMP PEAK  2(4P16.3) WILD-TYPE  5 25  6 12
D2V4, multiclass
    clus
vv   AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE
  T1                           4                             5
  T2                          23                            25
  T3                           5                             6
  T4                           8                            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"
D2V5, binary
                               cls
clus                             0  1
  AMP PEAK  2(4P16.3) MUTATED   36  4
  AMP PEAK  2(4P16.3) WILD-TYPE 42  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(4P16.3) MUTATED     36    4
  AMP PEAK  2(4P16.3) WILD-TYPE   42    6
   clus
vv  AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE
  0                          36                            42
  1                           4                             6
[1] 2 2
[1] FALSE
D2V6, binary
                               cls
clus                             0  1
  AMP PEAK  2(4P16.3) MUTATED   25 16
  AMP PEAK  2(4P16.3) WILD-TYPE 34 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(4P16.3) MUTATED     25   16
  AMP PEAK  2(4P16.3) WILD-TYPE   34   15
        clus
vv       AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE
  FEMALE                          25                            34
  MALE                            16                            15
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                             0  1
  AMP PEAK  2(4P16.3) MUTATED   33  7
  AMP PEAK  2(4P16.3) WILD-TYPE 36 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(4P16.3) MUTATED     33    7
  AMP PEAK  2(4P16.3) WILD-TYPE   36   11
     clus
vv    AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE
  NO                           33                            36
  YES                           7                            11
[1] 2 2
[1] FALSE
                               vv
clus                            ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AMP PEAK  2(4P16.3) MUTATED                                       1
  AMP PEAK  2(4P16.3) WILD-TYPE                                     0
                               vv
clus                            ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AMP PEAK  2(4P16.3) MUTATED                                          3
  AMP PEAK  2(4P16.3) WILD-TYPE                                        1
                               vv
clus                            ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AMP PEAK  2(4P16.3) MUTATED                                     37
  AMP PEAK  2(4P16.3) WILD-TYPE                                   48
D2V8, multiclass
                                          clus
vv                                         AMP PEAK  2(4P16.3) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                           3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                              37
                                          clus
vv                                         AMP PEAK  2(4P16.3) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                             1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  2(4P16.3) MUTATED   31  4  4  0
  AMP PEAK  2(4P16.3) WILD-TYPE 32  3  8  5
D2V9, multiclass
    clus
vv   AMP PEAK  2(4P16.3) MUTATED AMP PEAK  2(4P16.3) WILD-TYPE
  R0                          31                            32
  R1                           4                             3
  R2                           4                             8
  RX                           0                             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"
D2V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(4P16.3) MUTATED       1                         0    34
  AMP PEAK  2(4P16.3) WILD-TYPE     1                         1    42
D2V11, multiclass
                           clus
vv                          AMP PEAK  2(4P16.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              34
                           clus
vv                          AMP PEAK  2(4P16.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
                               cls
clus                             0  1
  AMP PEAK  2(4P16.3) MUTATED    4 14
  AMP PEAK  2(4P16.3) WILD-TYPE  4 24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(4P16.3) MUTATED      4   14
  AMP PEAK  2(4P16.3) WILD-TYPE    4   24
                        clus
vv                       AMP PEAK  2(4P16.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          14
                        clus
vv                       AMP PEAK  2(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            24
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(5P15.33) MUTATION ANALYSIS
D3V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  3(5P15.33) MUTATED   41 24
  AMP PEAK  3(5P15.33) WILD-TYPE 16  9
  AMP PEAK  3(5P15.33) MUTATED AMP PEAK  3(5P15.33) WILD-TYPE 
                            65                             25 
  AMP PEAK  3(5P15.33) MUTATED AMP PEAK  3(5P15.33) WILD-TYPE 
                            24                              9 
$`AMP PEAK  3(5P15.33) MUTATED`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 
       43.30        39.58        44.55        68.75        13.91        12.00 
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC 
       88.87        16.11        19.04        44.45        30.31        57.53 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       49.22        67.59        36.26       121.25        29.82        66.51 
TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       72.39        18.15        27.02       108.13        32.68       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       35.57        16.37        24.62        11.31        24.36        46.49 
TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 
       83.80       153.63        68.25        44.84         4.11        58.55 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       31.79        28.31        29.10        28.64        23.64         5.23 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK 
       14.63        52.24        78.41        14.33        36.33        90.08 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       53.03        61.08        77.00        79.07        61.05        28.04 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG 
       36.03        18.05        38.50         0.00        24.85 

$`AMP PEAK  3(5P15.33) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J2 TCGA-OR-A5JB 
       33.83        91.30        12.59        42.51        55.13        18.12 
TCGA-OR-A5JD TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JU 
       99.88        18.48        39.25        15.25        12.59         9.50 
TCGA-OR-A5JX TCGA-OR-A5K6 TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KY 
       31.23        49.08        88.01        95.18       127.50        12.85 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5LD TCGA-OR-A5LE TCGA-PK-A5H9 TCGA-PK-A5HA 
       60.89       152.15        39.35        21.76        20.25        39.48 
TCGA-PK-A5HC 
       22.32 

  AMP PEAK  3(5P15.33) MUTATED AMP PEAK  3(5P15.33) WILD-TYPE 
                           0.0                            9.5 
  AMP PEAK  3(5P15.33) MUTATED AMP PEAK  3(5P15.33) WILD-TYPE 
                        153.63                         152.15 
  AMP PEAK  3(5P15.33) MUTATED AMP PEAK  3(5P15.33) WILD-TYPE 
                         38.50                          39.25 
[1] "0.0 - 153.6 (38.5)" "9.5 - 152.2 (39.2)"
[1] "hr=" "1"  
D3V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  3(5P15.33) MUTATED         5       33        13       13
  AMP PEAK  3(5P15.33) WILD-TYPE       4       10         5        5
D3V3, multiclass
           clus
vv          AMP PEAK  3(5P15.33) MUTATED AMP PEAK  3(5P15.33) WILD-TYPE
  STAGE I                              5                              4
  STAGE II                            33                             10
  STAGE III                           13                              5
  STAGE IV                            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"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK  3(5P15.33) MUTATED    5 37  8 14
  AMP PEAK  3(5P15.33) WILD-TYPE  4 11  3  6
D3V4, multiclass
    clus
vv   AMP PEAK  3(5P15.33) MUTATED AMP PEAK  3(5P15.33) WILD-TYPE
  T1                            5                              4
  T2                           37                             11
  T3                            8                              3
  T4                           14                              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"
D3V5, binary
                                cls
clus                              0  1
  AMP PEAK  3(5P15.33) MUTATED   56  8
  AMP PEAK  3(5P15.33) WILD-TYPE 22  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(5P15.33) MUTATED     56    8
  AMP PEAK  3(5P15.33) WILD-TYPE   22    2
   clus
vv  AMP PEAK  3(5P15.33) MUTATED AMP PEAK  3(5P15.33) WILD-TYPE
  0                           56                             22
  1                            8                              2
[1] 2 2
[1] FALSE
D3V6, binary
                                cls
clus                              0  1
  AMP PEAK  3(5P15.33) MUTATED   41 24
  AMP PEAK  3(5P15.33) WILD-TYPE 18  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(5P15.33) MUTATED     41   24
  AMP PEAK  3(5P15.33) WILD-TYPE   18    7
        clus
vv       AMP PEAK  3(5P15.33) MUTATED AMP PEAK  3(5P15.33) WILD-TYPE
  FEMALE                           41                             18
  MALE                             24                              7
[1] 2 2
[1] FALSE
D3V7, binary
                                cls
clus                              0  1
  AMP PEAK  3(5P15.33) MUTATED   51 12
  AMP PEAK  3(5P15.33) WILD-TYPE 18  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(5P15.33) MUTATED     51   12
  AMP PEAK  3(5P15.33) WILD-TYPE   18    6
     clus
vv    AMP PEAK  3(5P15.33) MUTATED AMP PEAK  3(5P15.33) WILD-TYPE
  NO                            51                             18
  YES                           12                              6
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AMP PEAK  3(5P15.33) MUTATED                                       1
  AMP PEAK  3(5P15.33) WILD-TYPE                                     0
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AMP PEAK  3(5P15.33) MUTATED                                          3
  AMP PEAK  3(5P15.33) WILD-TYPE                                        1
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AMP PEAK  3(5P15.33) MUTATED                                     61
  AMP PEAK  3(5P15.33) WILD-TYPE                                   24
D3V8, multiclass
                                          clus
vv                                         AMP PEAK  3(5P15.33) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               61
                                          clus
vv                                         AMP PEAK  3(5P15.33) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  3(5P15.33) MUTATED   46  4  9  4
  AMP PEAK  3(5P15.33) WILD-TYPE 17  3  3  1
D3V9, multiclass
    clus
vv   AMP PEAK  3(5P15.33) MUTATED AMP PEAK  3(5P15.33) WILD-TYPE
  R0                           46                             17
  R1                            4                              3
  R2                            9                              3
  RX                            4                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(5P15.33) MUTATED       0                         1    55
  AMP PEAK  3(5P15.33) WILD-TYPE     2                         0    21
D3V11, multiclass
                           clus
vv                          AMP PEAK  3(5P15.33) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               55
                           clus
vv                          AMP PEAK  3(5P15.33) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                 21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
                                cls
clus                              0  1
  AMP PEAK  3(5P15.33) MUTATED    7 25
  AMP PEAK  3(5P15.33) WILD-TYPE  1 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(5P15.33) MUTATED      7   25
  AMP PEAK  3(5P15.33) WILD-TYPE    1   13
                        clus
vv                       AMP PEAK  3(5P15.33) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           25
                        clus
vv                       AMP PEAK  3(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             13
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(5Q35.3) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  4(5Q35.3) MUTATED   43 20
  AMP PEAK  4(5Q35.3) WILD-TYPE 14 13
  AMP PEAK  4(5Q35.3) MUTATED AMP PEAK  4(5Q35.3) WILD-TYPE 
                           63                            27 
  AMP PEAK  4(5Q35.3) MUTATED AMP PEAK  4(5Q35.3) WILD-TYPE 
                           20                            13 
$`AMP PEAK  4(5Q35.3) MUTATED`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 
       43.30        39.58        12.59        44.55        68.75        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC 
       12.00        88.87        16.11        44.45        30.31        57.53 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT 
       49.22        67.59        36.26       121.25        12.59        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 
       66.51        72.39        31.23        27.02       108.13       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS 
       35.57        16.37        24.62        24.36        46.49        83.80 
TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5L1 TCGA-OR-A5L4 TCGA-OR-A5L6 
      153.63        68.25        12.85        58.55        31.79        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LH 
       29.10        28.64        23.64         5.23        14.63        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO 
       36.33        90.08        53.03        61.08        77.00        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       61.05        28.04        36.03        18.05        38.50         0.00 
TCGA-PA-A5YG TCGA-PK-A5HA TCGA-PK-A5HC 
       24.85        39.48        22.32 

$`AMP PEAK  4(5Q35.3) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-PK-A5HB TCGA-OR-A5J2 TCGA-OR-A5J8 TCGA-OR-A5JB 
       33.83        91.30        42.51        55.13        19.04        18.12 
TCGA-OR-A5JD TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JU TCGA-OR-A5JY 
       99.88        18.48        39.25        15.25         9.50        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV 
       32.68        49.08        11.31        88.01        95.18       127.50 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5LD TCGA-OR-A5LE 
       44.84         4.11        60.89       152.15        39.35        21.76 
TCGA-OR-A5LG TCGA-OR-A5LI TCGA-PK-A5H9 
       52.24        14.33        20.25 

  AMP PEAK  4(5Q35.3) MUTATED AMP PEAK  4(5Q35.3) WILD-TYPE 
                         0.00                          4.11 
  AMP PEAK  4(5Q35.3) MUTATED AMP PEAK  4(5Q35.3) WILD-TYPE 
                       153.63                        152.15 
  AMP PEAK  4(5Q35.3) MUTATED AMP PEAK  4(5Q35.3) WILD-TYPE 
                        38.50                         39.25 
[1] "0.0 - 153.6 (38.5)" "4.1 - 152.2 (39.2)"
[1] "hr=" "1.6"
D4V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  4(5Q35.3) MUTATED         6       32        11       13
  AMP PEAK  4(5Q35.3) WILD-TYPE       3       11         7        5
D4V3, multiclass
           clus
vv          AMP PEAK  4(5Q35.3) MUTATED AMP PEAK  4(5Q35.3) WILD-TYPE
  STAGE I                             6                             3
  STAGE II                           32                            11
  STAGE III                          11                             7
  STAGE IV                           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"
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK  4(5Q35.3) MUTATED    6 35  7 14
  AMP PEAK  4(5Q35.3) WILD-TYPE  3 13  4  6
D4V4, multiclass
    clus
vv   AMP PEAK  4(5Q35.3) MUTATED AMP PEAK  4(5Q35.3) WILD-TYPE
  T1                           6                             3
  T2                          35                            13
  T3                           7                             4
  T4                          14                             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"
D4V5, binary
                               cls
clus                             0  1
  AMP PEAK  4(5Q35.3) MUTATED   55  7
  AMP PEAK  4(5Q35.3) WILD-TYPE 23  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q35.3) MUTATED     55    7
  AMP PEAK  4(5Q35.3) WILD-TYPE   23    3
   clus
vv  AMP PEAK  4(5Q35.3) MUTATED AMP PEAK  4(5Q35.3) WILD-TYPE
  0                          55                            23
  1                           7                             3
[1] 2 2
[1] FALSE
D4V6, binary
                               cls
clus                             0  1
  AMP PEAK  4(5Q35.3) MUTATED   40 23
  AMP PEAK  4(5Q35.3) WILD-TYPE 19  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q35.3) MUTATED     40   23
  AMP PEAK  4(5Q35.3) WILD-TYPE   19    8
        clus
vv       AMP PEAK  4(5Q35.3) MUTATED AMP PEAK  4(5Q35.3) WILD-TYPE
  FEMALE                          40                            19
  MALE                            23                             8
[1] 2 2
[1] FALSE
D4V7, binary
                               cls
clus                             0  1
  AMP PEAK  4(5Q35.3) MUTATED   50 11
  AMP PEAK  4(5Q35.3) WILD-TYPE 19  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q35.3) MUTATED     50   11
  AMP PEAK  4(5Q35.3) WILD-TYPE   19    7
     clus
vv    AMP PEAK  4(5Q35.3) MUTATED AMP PEAK  4(5Q35.3) WILD-TYPE
  NO                           50                            19
  YES                          11                             7
[1] 2 2
[1] FALSE
                               vv
clus                            ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AMP PEAK  4(5Q35.3) MUTATED                                       1
  AMP PEAK  4(5Q35.3) WILD-TYPE                                     0
                               vv
clus                            ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AMP PEAK  4(5Q35.3) MUTATED                                          3
  AMP PEAK  4(5Q35.3) WILD-TYPE                                        1
                               vv
clus                            ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AMP PEAK  4(5Q35.3) MUTATED                                     59
  AMP PEAK  4(5Q35.3) WILD-TYPE                                   26
D4V8, multiclass
                                          clus
vv                                         AMP PEAK  4(5Q35.3) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                           3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                              59
                                          clus
vv                                         AMP PEAK  4(5Q35.3) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                             1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  4(5Q35.3) MUTATED   45  5  9  2
  AMP PEAK  4(5Q35.3) WILD-TYPE 18  2  3  3
D4V9, multiclass
    clus
vv   AMP PEAK  4(5Q35.3) MUTATED AMP PEAK  4(5Q35.3) WILD-TYPE
  R0                          45                            18
  R1                           5                             2
  R2                           9                             3
  RX                           2                             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"
D4V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(5Q35.3) MUTATED       1                         1    51
  AMP PEAK  4(5Q35.3) WILD-TYPE     1                         0    25
D4V11, multiclass
                           clus
vv                          AMP PEAK  4(5Q35.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              51
                           clus
vv                          AMP PEAK  4(5Q35.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
                               cls
clus                             0  1
  AMP PEAK  4(5Q35.3) MUTATED    6 24
  AMP PEAK  4(5Q35.3) WILD-TYPE  2 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q35.3) MUTATED      6   24
  AMP PEAK  4(5Q35.3) WILD-TYPE    2   14
                        clus
vv                       AMP PEAK  4(5Q35.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          24
                        clus
vv                       AMP PEAK  4(5Q35.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            14
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(6P21.31) MUTATION ANALYSIS
D5V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  5(6P21.31) MUTATED   11  8
  AMP PEAK  5(6P21.31) WILD-TYPE 46 25
  AMP PEAK  5(6P21.31) MUTATED AMP PEAK  5(6P21.31) WILD-TYPE 
                            19                             71 
  AMP PEAK  5(6P21.31) MUTATED AMP PEAK  5(6P21.31) WILD-TYPE 
                             8                             25 
$`AMP PEAK  5(6P21.31) MUTATED`
TCGA-OR-A5KP TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC 
       91.30        13.91        88.87        16.11        30.31        57.53 
TCGA-OR-A5JE TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KZ 
       69.21        67.59        18.48        24.36        46.49         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L4 TCGA-OR-A5LI TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN 
       58.55        31.79        14.33        90.08        61.08        77.00 
TCGA-PK-A5HC 
       22.32 

$`AMP PEAK  5(6P21.31) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        43.30        39.58        12.59        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB 
       55.13        68.75        12.00        19.04        44.45        18.12 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       99.88        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JK TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       49.22        39.25        15.25        36.26       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       29.82         9.50        66.51        72.39        31.23        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       27.02       108.13        32.68       113.92        35.57        16.37 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       49.08        24.62        11.31        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L2 
      153.63       127.50        68.25        44.84        12.85        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
      152.15        28.31        29.10        28.64        23.64         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        79.07        61.05        28.04        36.03        18.05 
TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       38.50         0.00        24.85        20.25        39.48 

  AMP PEAK  5(6P21.31) MUTATED AMP PEAK  5(6P21.31) WILD-TYPE 
                          4.11                           0.00 
  AMP PEAK  5(6P21.31) MUTATED AMP PEAK  5(6P21.31) WILD-TYPE 
                         91.30                         153.63 
  AMP PEAK  5(6P21.31) MUTATED AMP PEAK  5(6P21.31) WILD-TYPE 
                         46.49                          38.50 
[1] "4.1 - 91.3 (46.5)"  "0.0 - 153.6 (38.5)"
[1] "hr=" "1.1"
D5V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  5(6P21.31) MUTATED         2        8         3        5
  AMP PEAK  5(6P21.31) WILD-TYPE       7       35        15       13
D5V3, multiclass
           clus
vv          AMP PEAK  5(6P21.31) MUTATED AMP PEAK  5(6P21.31) WILD-TYPE
  STAGE I                              2                              7
  STAGE II                             8                             35
  STAGE III                            3                             15
  STAGE IV                             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"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK  5(6P21.31) MUTATED    2  8  2  6
  AMP PEAK  5(6P21.31) WILD-TYPE  7 40  9 14
D5V4, multiclass
    clus
vv   AMP PEAK  5(6P21.31) MUTATED AMP PEAK  5(6P21.31) WILD-TYPE
  T1                            2                              7
  T2                            8                             40
  T3                            2                              9
  T4                            6                             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"
D5V5, binary
                                cls
clus                              0  1
  AMP PEAK  5(6P21.31) MUTATED   17  1
  AMP PEAK  5(6P21.31) WILD-TYPE 61  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(6P21.31) MUTATED     17    1
  AMP PEAK  5(6P21.31) WILD-TYPE   61    9
   clus
vv  AMP PEAK  5(6P21.31) MUTATED AMP PEAK  5(6P21.31) WILD-TYPE
  0                           17                             61
  1                            1                              9
[1] 2 2
[1] FALSE
D5V6, binary
                                cls
clus                              0  1
  AMP PEAK  5(6P21.31) MUTATED   15  4
  AMP PEAK  5(6P21.31) WILD-TYPE 44 27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(6P21.31) MUTATED     15    4
  AMP PEAK  5(6P21.31) WILD-TYPE   44   27
        clus
vv       AMP PEAK  5(6P21.31) MUTATED AMP PEAK  5(6P21.31) WILD-TYPE
  FEMALE                           15                             44
  MALE                              4                             27
[1] 2 2
[1] FALSE
D5V7, binary
                                cls
clus                              0  1
  AMP PEAK  5(6P21.31) MUTATED   17  1
  AMP PEAK  5(6P21.31) WILD-TYPE 52 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(6P21.31) MUTATED     17    1
  AMP PEAK  5(6P21.31) WILD-TYPE   52   17
     clus
vv    AMP PEAK  5(6P21.31) MUTATED AMP PEAK  5(6P21.31) WILD-TYPE
  NO                            17                             52
  YES                            1                             17
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AMP PEAK  5(6P21.31) MUTATED                                       0
  AMP PEAK  5(6P21.31) WILD-TYPE                                     1
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AMP PEAK  5(6P21.31) MUTATED                                          1
  AMP PEAK  5(6P21.31) WILD-TYPE                                        3
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AMP PEAK  5(6P21.31) MUTATED                                     18
  AMP PEAK  5(6P21.31) WILD-TYPE                                   67
D5V8, multiclass
                                          clus
vv                                         AMP PEAK  5(6P21.31) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               18
                                          clus
vv                                         AMP PEAK  5(6P21.31) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  5(6P21.31) MUTATED   10  4  2  2
  AMP PEAK  5(6P21.31) WILD-TYPE 53  3 10  3
D5V9, multiclass
    clus
vv   AMP PEAK  5(6P21.31) MUTATED AMP PEAK  5(6P21.31) WILD-TYPE
  R0                           10                             53
  R1                            4                              3
  R2                            2                             10
  RX                            2                              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"
D5V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(6P21.31) MUTATED       1                         1    14
  AMP PEAK  5(6P21.31) WILD-TYPE     1                         0    62
D5V11, multiclass
                           clus
vv                          AMP PEAK  5(6P21.31) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               14
                           clus
vv                          AMP PEAK  5(6P21.31) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                 62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
                                cls
clus                              0  1
  AMP PEAK  5(6P21.31) MUTATED    3  8
  AMP PEAK  5(6P21.31) WILD-TYPE  5 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(6P21.31) MUTATED      3    8
  AMP PEAK  5(6P21.31) WILD-TYPE    5   30
                        clus
vv                       AMP PEAK  5(6P21.31) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                            8
                        clus
vv                       AMP PEAK  5(6P21.31) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             30
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(6Q24.3) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  6(6Q24.3) MUTATED   12  7
  AMP PEAK  6(6Q24.3) WILD-TYPE 45 26
  AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE 
                           19                            71 
  AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE 
                            7                            26 
$`AMP PEAK  6(6Q24.3) MUTATED`
TCGA-OR-A5K0 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE 
       33.83        88.87        19.04        30.31        57.53        69.21 
TCGA-OR-A5JL TCGA-OR-A5K2 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KZ 
       67.59        32.68        24.62        24.36        46.49         4.11 
TCGA-OR-A5L4 TCGA-OR-A5LI TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-PK-A5HA 
       31.79        14.33        90.08        61.08        77.00        39.48 
TCGA-PK-A5HC 
       22.32 

$`AMP PEAK  6(6Q24.3) WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 
       91.30        43.30        39.58        12.59        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J9 
       55.13        68.75        13.91        12.00        16.11        44.45 
TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        99.88        66.25        17.79        69.37        76.64 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       16.11        49.22        18.48        39.25        15.25        36.26 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW 
      121.25        12.59        29.82         9.50        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 
       31.23        18.15        27.02       108.13       113.92        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       16.37        49.08        11.31        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L1 
      153.63       127.50        68.25        44.84        12.85        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       60.89       152.15        28.31        29.10        28.64        23.64 
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-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       36.33        53.03        79.07        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 
       18.05        38.50         0.00        24.85        20.25 

  AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE 
                         4.11                          0.00 
  AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE 
                        90.08                        153.63 
  AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE 
                        33.83                         39.25 
[1] "4.1 - 90.1 (33.8)"  "0.0 - 153.6 (39.2)"
[1] "hr=" "1"  
D6V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  6(6Q24.3) MUTATED         3        8         4        3
  AMP PEAK  6(6Q24.3) WILD-TYPE       6       35        14       15
D6V3, multiclass
           clus
vv          AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE
  STAGE I                             3                             6
  STAGE II                            8                            35
  STAGE III                           4                            14
  STAGE IV                            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"
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK  6(6Q24.3) MUTATED    3  8  1  6
  AMP PEAK  6(6Q24.3) WILD-TYPE  6 40 10 14
D6V4, multiclass
    clus
vv   AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE
  T1                           3                             6
  T2                           8                            40
  T3                           1                            10
  T4                           6                            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(6Q24.3) MUTATED   18  0
  AMP PEAK  6(6Q24.3) WILD-TYPE 60 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(6Q24.3) MUTATED     18    0
  AMP PEAK  6(6Q24.3) WILD-TYPE   60   10
   clus
vv  AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE
  0                          18                            60
  1                           0                            10
[1] 2 2
[1] FALSE
D6V6, binary
                               cls
clus                             0  1
  AMP PEAK  6(6Q24.3) MUTATED   12  7
  AMP PEAK  6(6Q24.3) WILD-TYPE 47 24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(6Q24.3) MUTATED     12    7
  AMP PEAK  6(6Q24.3) WILD-TYPE   47   24
        clus
vv       AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE
  FEMALE                          12                            47
  MALE                             7                            24
[1] 2 2
[1] FALSE
D6V7, binary
                               cls
clus                             0  1
  AMP PEAK  6(6Q24.3) MUTATED   16  2
  AMP PEAK  6(6Q24.3) WILD-TYPE 53 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(6Q24.3) MUTATED     16    2
  AMP PEAK  6(6Q24.3) WILD-TYPE   53   16
     clus
vv    AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE
  NO                           16                            53
  YES                           2                            16
[1] 2 2
[1] FALSE
                               vv
clus                            ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AMP PEAK  6(6Q24.3) MUTATED                                       0
  AMP PEAK  6(6Q24.3) WILD-TYPE                                     1
                               vv
clus                            ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AMP PEAK  6(6Q24.3) MUTATED                                          1
  AMP PEAK  6(6Q24.3) WILD-TYPE                                        3
                               vv
clus                            ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AMP PEAK  6(6Q24.3) MUTATED                                     18
  AMP PEAK  6(6Q24.3) WILD-TYPE                                   67
D6V8, multiclass
                                          clus
vv                                         AMP PEAK  6(6Q24.3) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                              0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                           1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                              18
                                          clus
vv                                         AMP PEAK  6(6Q24.3) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                             3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  6(6Q24.3) MUTATED   13  2  1  2
  AMP PEAK  6(6Q24.3) WILD-TYPE 50  5 11  3
D6V9, multiclass
    clus
vv   AMP PEAK  6(6Q24.3) MUTATED AMP PEAK  6(6Q24.3) WILD-TYPE
  R0                          13                            50
  R1                           2                             5
  R2                           1                            11
  RX                           2                             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"
D6V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(6Q24.3) MUTATED       1                         1    13
  AMP PEAK  6(6Q24.3) WILD-TYPE     1                         0    63
D6V11, multiclass
                           clus
vv                          AMP PEAK  6(6Q24.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              13
                           clus
vv                          AMP PEAK  6(6Q24.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, binary
                               cls
clus                             0  1
  AMP PEAK  6(6Q24.3) MUTATED    2  7
  AMP PEAK  6(6Q24.3) WILD-TYPE  6 31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(6Q24.3) MUTATED      2    7
  AMP PEAK  6(6Q24.3) WILD-TYPE    6   31
                        clus
vv                       AMP PEAK  6(6Q24.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                           7
                        clus
vv                       AMP PEAK  6(6Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            31
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(7P22.1) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  7(7P22.1) MUTATED   32 22
  AMP PEAK  7(7P22.1) WILD-TYPE 25 11
  AMP PEAK  7(7P22.1) MUTATED AMP PEAK  7(7P22.1) WILD-TYPE 
                           54                            36 
  AMP PEAK  7(7P22.1) MUTATED AMP PEAK  7(7P22.1) WILD-TYPE 
                           22                            11 
$`AMP PEAK  7(7P22.1) MUTATED`
TCGA-OR-A5LB TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       39.58        55.13        68.75        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JJ 
       19.04        30.31        66.25        17.79        69.37        16.11 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       49.22        67.59        36.26       121.25        29.82        66.51 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K6 
       31.23        18.15       108.13       113.92        16.37        49.08 
TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX 
       24.62        46.49        83.80       153.63        68.25        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L8 
       12.85         4.11        58.55        60.89        31.79        29.10 
TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LH 
       23.64         5.23        39.35        21.76        14.63        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO 
       36.33        90.08        53.03        61.08        77.00        79.07 
TCGA-OR-A5LP TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5HC 
       61.05        36.03        38.50         0.00        24.85        22.32 

$`AMP PEAK  7(7P22.1) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        43.30        12.59        42.51        44.55 
TCGA-OR-A5J4 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       13.91        44.45        18.12        57.53        99.88        69.21 
TCGA-OR-A5JI TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JU 
       76.64        18.48        39.25        15.25        12.59         9.50 
TCGA-OR-A5JW TCGA-OR-A5JZ TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K9 TCGA-OR-A5KB 
       72.39        27.02        32.68        35.57        11.31        24.36 
TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5L3 TCGA-OR-A5L6 TCGA-OR-A5L9 
       88.01        95.18       127.50       152.15        28.31        28.64 
TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LR TCGA-OR-A5LT TCGA-PK-A5H9 TCGA-PK-A5HA 
       52.24        14.33        28.04        18.05        20.25        39.48 

  AMP PEAK  7(7P22.1) MUTATED AMP PEAK  7(7P22.1) WILD-TYPE 
                          0.0                           9.5 
  AMP PEAK  7(7P22.1) MUTATED AMP PEAK  7(7P22.1) WILD-TYPE 
                       153.63                        152.15 
  AMP PEAK  7(7P22.1) MUTATED AMP PEAK  7(7P22.1) WILD-TYPE 
                       39.465                        34.700 
[1] "0.0 - 153.6 (39.5)" "9.5 - 152.2 (34.7)"
[1] "hr=" "1.2"
D7V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  7(7P22.1) MUTATED         2       27        12       13
  AMP PEAK  7(7P22.1) WILD-TYPE       7       16         6        5
D7V3, multiclass
           clus
vv          AMP PEAK  7(7P22.1) MUTATED AMP PEAK  7(7P22.1) WILD-TYPE
  STAGE I                             2                             7
  STAGE II                           27                            16
  STAGE III                          12                             6
  STAGE IV                           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"
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK  7(7P22.1) MUTATED    2 31  7 14
  AMP PEAK  7(7P22.1) WILD-TYPE  7 17  4  6
D7V4, multiclass
    clus
vv   AMP PEAK  7(7P22.1) MUTATED AMP PEAK  7(7P22.1) WILD-TYPE
  T1                           2                             7
  T2                          31                            17
  T3                           7                             4
  T4                          14                             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"
D7V5, binary
                               cls
clus                             0  1
  AMP PEAK  7(7P22.1) MUTATED   46  8
  AMP PEAK  7(7P22.1) WILD-TYPE 32  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7P22.1) MUTATED     46    8
  AMP PEAK  7(7P22.1) WILD-TYPE   32    2
   clus
vv  AMP PEAK  7(7P22.1) MUTATED AMP PEAK  7(7P22.1) WILD-TYPE
  0                          46                            32
  1                           8                             2
[1] 2 2
[1] FALSE
D7V6, binary
                               cls
clus                             0  1
  AMP PEAK  7(7P22.1) MUTATED   35 19
  AMP PEAK  7(7P22.1) WILD-TYPE 24 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7P22.1) MUTATED     35   19
  AMP PEAK  7(7P22.1) WILD-TYPE   24   12
        clus
vv       AMP PEAK  7(7P22.1) MUTATED AMP PEAK  7(7P22.1) WILD-TYPE
  FEMALE                          35                            24
  MALE                            19                            12
[1] 2 2
[1] FALSE
D7V7, binary
                               cls
clus                             0  1
  AMP PEAK  7(7P22.1) MUTATED   44  9
  AMP PEAK  7(7P22.1) WILD-TYPE 25  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7P22.1) MUTATED     44    9
  AMP PEAK  7(7P22.1) WILD-TYPE   25    9
     clus
vv    AMP PEAK  7(7P22.1) MUTATED AMP PEAK  7(7P22.1) WILD-TYPE
  NO                           44                            25
  YES                           9                             9
[1] 2 2
[1] FALSE
                               vv
clus                            ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AMP PEAK  7(7P22.1) MUTATED                                       1
  AMP PEAK  7(7P22.1) WILD-TYPE                                     0
                               vv
clus                            ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AMP PEAK  7(7P22.1) MUTATED                                          3
  AMP PEAK  7(7P22.1) WILD-TYPE                                        1
                               vv
clus                            ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AMP PEAK  7(7P22.1) MUTATED                                     50
  AMP PEAK  7(7P22.1) WILD-TYPE                                   35
D7V8, multiclass
                                          clus
vv                                         AMP PEAK  7(7P22.1) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                           3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                              50
                                          clus
vv                                         AMP PEAK  7(7P22.1) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                             1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  7(7P22.1) MUTATED   36  4  9  4
  AMP PEAK  7(7P22.1) WILD-TYPE 27  3  3  1
D7V9, multiclass
    clus
vv   AMP PEAK  7(7P22.1) MUTATED AMP PEAK  7(7P22.1) WILD-TYPE
  R0                          36                            27
  R1                           4                             3
  R2                           9                             3
  RX                           4                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(7P22.1) MUTATED       1                         1    45
  AMP PEAK  7(7P22.1) WILD-TYPE     1                         0    31
D7V11, multiclass
                           clus
vv                          AMP PEAK  7(7P22.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              45
                           clus
vv                          AMP PEAK  7(7P22.1) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
                               cls
clus                             0  1
  AMP PEAK  7(7P22.1) MUTATED    6 25
  AMP PEAK  7(7P22.1) WILD-TYPE  2 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7P22.1) MUTATED      6   25
  AMP PEAK  7(7P22.1) WILD-TYPE    2   13
                        clus
vv                       AMP PEAK  7(7P22.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          25
                        clus
vv                       AMP PEAK  7(7P22.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            13
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(9Q31.3) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  8(9Q31.3) MUTATED   17 17
  AMP PEAK  8(9Q31.3) WILD-TYPE 40 16
  AMP PEAK  8(9Q31.3) MUTATED AMP PEAK  8(9Q31.3) WILD-TYPE 
                           34                            56 
  AMP PEAK  8(9Q31.3) MUTATED AMP PEAK  8(9Q31.3) WILD-TYPE 
                           17                            16 
$`AMP PEAK  8(9Q31.3) MUTATED`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5LB TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 
       33.83        91.30        39.58        13.91        12.00        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       19.04        44.45        30.31        69.21        66.25        17.79 
TCGA-OR-A5JH TCGA-OR-A5JJ TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5K2 TCGA-OR-A5K8 
       69.37        16.11        36.26        66.51        32.68        24.62 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
       24.36        46.49        83.80        44.84        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5LC TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LS 
       58.55         5.23        14.33        36.33        53.03        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PK-A5HC 
       18.05        38.50         0.00        22.32 

$`AMP PEAK  8(9Q31.3) WILD-TYPE`
TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       43.30        12.59        42.51        44.55        55.13        68.75 
TCGA-OR-A5J6 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JI TCGA-OR-A5JK 
       88.87        18.12        57.53        99.88        76.64        49.22 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS 
       67.59        18.48        39.25        15.25       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ 
       29.82         9.50        72.39        31.23        18.15        27.02 
TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
      108.13       113.92        35.57        16.37        49.08        11.31 
TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5L2 
       88.01        95.18       153.63       127.50        68.25        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        28.31        29.10        28.64        23.64 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LK 
       39.35        21.76        14.63        52.24        78.41        90.08 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG 
       61.08        77.00        79.07        61.05        28.04        24.85 
TCGA-PK-A5H9 TCGA-PK-A5HA 
       20.25        39.48 

  AMP PEAK  8(9Q31.3) MUTATED AMP PEAK  8(9Q31.3) WILD-TYPE 
                          0.0                           9.5 
  AMP PEAK  8(9Q31.3) MUTATED AMP PEAK  8(9Q31.3) WILD-TYPE 
                        91.30                        153.63 
  AMP PEAK  8(9Q31.3) MUTATED AMP PEAK  8(9Q31.3) WILD-TYPE 
                       33.255                        43.925 
[1] "0.0 - 91.3 (33.3)"  "9.5 - 153.6 (43.9)"
[1] "hr=" "2.4"
D8V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  8(9Q31.3) MUTATED         1       14         7       12
  AMP PEAK  8(9Q31.3) WILD-TYPE       8       29        11        6
D8V3, multiclass
           clus
vv          AMP PEAK  8(9Q31.3) MUTATED AMP PEAK  8(9Q31.3) WILD-TYPE
  STAGE I                             1                             8
  STAGE II                           14                            29
  STAGE III                           7                            11
  STAGE IV                           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"
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK  8(9Q31.3) MUTATED    1 17  4 12
  AMP PEAK  8(9Q31.3) WILD-TYPE  8 31  7  8
D8V4, multiclass
    clus
vv   AMP PEAK  8(9Q31.3) MUTATED AMP PEAK  8(9Q31.3) WILD-TYPE
  T1                           1                             8
  T2                          17                            31
  T3                           4                             7
  T4                          12                             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"
D8V5, binary
                               cls
clus                             0  1
  AMP PEAK  8(9Q31.3) MUTATED   27  7
  AMP PEAK  8(9Q31.3) WILD-TYPE 51  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(9Q31.3) MUTATED     27    7
  AMP PEAK  8(9Q31.3) WILD-TYPE   51    3
   clus
vv  AMP PEAK  8(9Q31.3) MUTATED AMP PEAK  8(9Q31.3) WILD-TYPE
  0                          27                            51
  1                           7                             3
[1] 2 2
[1] FALSE
D8V6, binary
                               cls
clus                             0  1
  AMP PEAK  8(9Q31.3) MUTATED   24 10
  AMP PEAK  8(9Q31.3) WILD-TYPE 35 21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(9Q31.3) MUTATED     24   10
  AMP PEAK  8(9Q31.3) WILD-TYPE   35   21
        clus
vv       AMP PEAK  8(9Q31.3) MUTATED AMP PEAK  8(9Q31.3) WILD-TYPE
  FEMALE                          24                            35
  MALE                            10                            21
[1] 2 2
[1] FALSE
D8V7, binary
                               cls
clus                             0  1
  AMP PEAK  8(9Q31.3) MUTATED   29  4
  AMP PEAK  8(9Q31.3) WILD-TYPE 40 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(9Q31.3) MUTATED     29    4
  AMP PEAK  8(9Q31.3) WILD-TYPE   40   14
     clus
vv    AMP PEAK  8(9Q31.3) MUTATED AMP PEAK  8(9Q31.3) WILD-TYPE
  NO                           29                            40
  YES                           4                            14
[1] 2 2
[1] FALSE
                               vv
clus                            ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AMP PEAK  8(9Q31.3) MUTATED                                       1
  AMP PEAK  8(9Q31.3) WILD-TYPE                                     0
                               vv
clus                            ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AMP PEAK  8(9Q31.3) MUTATED                                          1
  AMP PEAK  8(9Q31.3) WILD-TYPE                                        3
                               vv
clus                            ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AMP PEAK  8(9Q31.3) MUTATED                                     32
  AMP PEAK  8(9Q31.3) WILD-TYPE                                   53
D8V8, multiclass
                                          clus
vv                                         AMP PEAK  8(9Q31.3) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                           1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                              32
                                          clus
vv                                         AMP PEAK  8(9Q31.3) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                             3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  8(9Q31.3) MUTATED   20  4  8  1
  AMP PEAK  8(9Q31.3) WILD-TYPE 43  3  4  4
D8V9, multiclass
    clus
vv   AMP PEAK  8(9Q31.3) MUTATED AMP PEAK  8(9Q31.3) WILD-TYPE
  R0                          20                            43
  R1                           4                             3
  R2                           8                             4
  RX                           1                             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"
D8V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(9Q31.3) MUTATED       1                         0    30
  AMP PEAK  8(9Q31.3) WILD-TYPE     1                         1    46
D8V11, multiclass
                           clus
vv                          AMP PEAK  8(9Q31.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              30
                           clus
vv                          AMP PEAK  8(9Q31.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
                               cls
clus                             0  1
  AMP PEAK  8(9Q31.3) MUTATED    5 16
  AMP PEAK  8(9Q31.3) WILD-TYPE  3 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(9Q31.3) MUTATED      5   16
  AMP PEAK  8(9Q31.3) WILD-TYPE    3   22
                        clus
vv                       AMP PEAK  8(9Q31.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          16
                        clus
vv                       AMP PEAK  8(9Q31.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            22
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(12Q14.1) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  9(12Q14.1) MUTATED   43 27
  AMP PEAK  9(12Q14.1) WILD-TYPE 14  6
  AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE 
                            70                             20 
  AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE 
                            27                              6 
$`AMP PEAK  9(12Q14.1) MUTATED`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 
       91.30        43.30        39.58        55.13        68.75        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA 
       12.00        88.87        16.11        19.04        44.45        30.31 
TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
       57.53        69.21        66.25        17.79        69.37        76.64 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JQ 
       16.11        49.22        67.59        18.48        15.25        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ 
      121.25        29.82        66.51        31.23        18.15        27.02 
TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 
      108.13        32.68       113.92        35.57        16.37        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX 
       11.31        83.80        95.18       153.63        68.25        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L6 
       12.85         4.11        58.55        60.89        31.79        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LF 
       29.10        28.64        23.64         5.23        39.35        14.63 
TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN 
       78.41        14.33        36.33        90.08        61.08        77.00 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       79.07        61.05        28.04        36.03        18.05        38.50 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5HA TCGA-PK-A5HC 
        0.00        24.85        39.48        22.32 

$`AMP PEAK  9(12Q14.1) WILD-TYPE`
TCGA-OR-A5K0 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5JB TCGA-OR-A5JD 
       33.83        12.59        42.51        44.55        18.12        99.88 
TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5K6 TCGA-OR-A5KB 
       39.25        12.59         9.50        72.39        49.08        24.36 
TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KV TCGA-OR-A5L3 TCGA-OR-A5LE TCGA-OR-A5LG 
       46.49        88.01       127.50       152.15        21.76        52.24 
TCGA-OR-A5LL TCGA-PK-A5H9 
       53.03        20.25 

  AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE 
                           0.0                            9.5 
  AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE 
                        153.63                         152.15 
  AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE 
                        36.295                         43.530 
[1] "0.0 - 153.6 (36.3)" "9.5 - 152.2 (43.5)"
[1] "hr=" "1.3"
D9V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  9(12Q14.1) MUTATED         7       32        15       15
  AMP PEAK  9(12Q14.1) WILD-TYPE       2       11         3        3
D9V3, multiclass
           clus
vv          AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE
  STAGE I                              7                              2
  STAGE II                            32                             11
  STAGE III                           15                              3
  STAGE IV                            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"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK  9(12Q14.1) MUTATED    7 36  9 17
  AMP PEAK  9(12Q14.1) WILD-TYPE  2 12  2  3
D9V4, multiclass
    clus
vv   AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE
  T1                            7                              2
  T2                           36                             12
  T3                            9                              2
  T4                           17                              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"
D9V5, binary
                                cls
clus                              0  1
  AMP PEAK  9(12Q14.1) MUTATED   60  9
  AMP PEAK  9(12Q14.1) WILD-TYPE 18  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12Q14.1) MUTATED     60    9
  AMP PEAK  9(12Q14.1) WILD-TYPE   18    1
   clus
vv  AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE
  0                           60                             18
  1                            9                              1
[1] 2 2
[1] FALSE
D9V6, binary
                                cls
clus                              0  1
  AMP PEAK  9(12Q14.1) MUTATED   45 25
  AMP PEAK  9(12Q14.1) WILD-TYPE 14  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12Q14.1) MUTATED     45   25
  AMP PEAK  9(12Q14.1) WILD-TYPE   14    6
        clus
vv       AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE
  FEMALE                           45                             14
  MALE                             25                              6
[1] 2 2
[1] FALSE
D9V7, binary
                                cls
clus                              0  1
  AMP PEAK  9(12Q14.1) MUTATED   55 13
  AMP PEAK  9(12Q14.1) WILD-TYPE 14  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12Q14.1) MUTATED     55   13
  AMP PEAK  9(12Q14.1) WILD-TYPE   14    5
     clus
vv    AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE
  NO                            55                             14
  YES                           13                              5
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AMP PEAK  9(12Q14.1) MUTATED                                       1
  AMP PEAK  9(12Q14.1) WILD-TYPE                                     0
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AMP PEAK  9(12Q14.1) MUTATED                                          3
  AMP PEAK  9(12Q14.1) WILD-TYPE                                        1
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AMP PEAK  9(12Q14.1) MUTATED                                     66
  AMP PEAK  9(12Q14.1) WILD-TYPE                                   19
D9V8, multiclass
                                          clus
vv                                         AMP PEAK  9(12Q14.1) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               66
                                          clus
vv                                         AMP PEAK  9(12Q14.1) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  9(12Q14.1) MUTATED   47  6 11  4
  AMP PEAK  9(12Q14.1) WILD-TYPE 16  1  1  1
D9V9, multiclass
    clus
vv   AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE
  R0                           47                             16
  R1                            6                              1
  R2                           11                              1
  RX                            4                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(12Q14.1) MUTATED       1                         1    59
  AMP PEAK  9(12Q14.1) WILD-TYPE     1                         0    17
D9V11, multiclass
                           clus
vv                          AMP PEAK  9(12Q14.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               59
                           clus
vv                          AMP PEAK  9(12Q14.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                 17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
                                cls
clus                              0  1
  AMP PEAK  9(12Q14.1) MUTATED    8 28
  AMP PEAK  9(12Q14.1) WILD-TYPE  0 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12Q14.1) MUTATED      8   28
  AMP PEAK  9(12Q14.1) WILD-TYPE    0   10
                        clus
vv                       AMP PEAK  9(12Q14.1) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           28
                        clus
vv                       AMP PEAK  9(12Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                             10
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(14Q11.2) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 10(14Q11.2) MUTATED   15 12
  AMP PEAK 10(14Q11.2) WILD-TYPE 42 21
  AMP PEAK 10(14Q11.2) MUTATED AMP PEAK 10(14Q11.2) WILD-TYPE 
                            27                             63 
  AMP PEAK 10(14Q11.2) MUTATED AMP PEAK 10(14Q11.2) WILD-TYPE 
                            12                             21 
$`AMP PEAK 10(14Q11.2) MUTATED`
TCGA-OR-A5KP TCGA-OR-A5LB TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J9 
       91.30        39.58        68.75        13.91        12.00        44.45 
TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JJ TCGA-OR-A5JL 
       30.31        57.53        69.21        17.79        16.11        67.59 
TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KW TCGA-OR-A5KX 
       18.48        15.25        24.62        46.49        68.25        44.84 
TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO 
       60.89        31.79        29.10        53.03        61.08        79.07 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HC 
       36.03        38.50        22.32 

$`AMP PEAK 10(14Q11.2) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       33.83        43.30        12.59        42.51        44.55        55.13 
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JF 
       88.87        16.11        19.04        18.12        99.88        66.25 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR 
       69.37        76.64        49.22        39.25        36.26       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        29.82         9.50        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
       18.15        27.02       108.13        32.68       113.92        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KQ TCGA-OR-A5KS 
       16.37        49.08        11.31        24.36        88.01        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
       95.18       153.63       127.50        12.85         4.11        58.55 
TCGA-OR-A5L3 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
      152.15        28.31        28.64        23.64         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ 
       21.76        14.63        52.24        78.41        14.33        36.33 
TCGA-OR-A5LK TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OH 
       90.08        77.00        61.05        28.04        18.05         0.00 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       24.85        20.25        39.48 

  AMP PEAK 10(14Q11.2) MUTATED AMP PEAK 10(14Q11.2) WILD-TYPE 
                            12                              0 
  AMP PEAK 10(14Q11.2) MUTATED AMP PEAK 10(14Q11.2) WILD-TYPE 
                         91.30                         153.63 
  AMP PEAK 10(14Q11.2) MUTATED AMP PEAK 10(14Q11.2) WILD-TYPE 
                         39.58                          36.33 
[1] "12.0 - 91.3 (39.6)" "0.0 - 153.6 (36.3)"
[1] "hr=" "1.4"
D10V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 10(14Q11.2) MUTATED         2       10         6        8
  AMP PEAK 10(14Q11.2) WILD-TYPE       7       33        12       10
D10V3, multiclass
           clus
vv          AMP PEAK 10(14Q11.2) MUTATED AMP PEAK 10(14Q11.2) WILD-TYPE
  STAGE I                              2                              7
  STAGE II                            10                             33
  STAGE III                            6                             12
  STAGE IV                             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"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 10(14Q11.2) MUTATED    2 13  2  9
  AMP PEAK 10(14Q11.2) WILD-TYPE  7 35  9 11
D10V4, multiclass
    clus
vv   AMP PEAK 10(14Q11.2) MUTATED AMP PEAK 10(14Q11.2) WILD-TYPE
  T1                            2                              7
  T2                           13                             35
  T3                            2                              9
  T4                            9                             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"
D10V5, binary
                                cls
clus                              0  1
  AMP PEAK 10(14Q11.2) MUTATED   20  6
  AMP PEAK 10(14Q11.2) WILD-TYPE 58  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(14Q11.2) MUTATED     20    6
  AMP PEAK 10(14Q11.2) WILD-TYPE   58    4
   clus
vv  AMP PEAK 10(14Q11.2) MUTATED AMP PEAK 10(14Q11.2) WILD-TYPE
  0                           20                             58
  1                            6                              4
[1] 2 2
[1] FALSE
D10V6, binary
                                cls
clus                              0  1
  AMP PEAK 10(14Q11.2) MUTATED   19  8
  AMP PEAK 10(14Q11.2) WILD-TYPE 40 23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(14Q11.2) MUTATED     19    8
  AMP PEAK 10(14Q11.2) WILD-TYPE   40   23
        clus
vv       AMP PEAK 10(14Q11.2) MUTATED AMP PEAK 10(14Q11.2) WILD-TYPE
  FEMALE                           19                             40
  MALE                              8                             23
[1] 2 2
[1] FALSE
D10V7, binary
                                cls
clus                              0  1
  AMP PEAK 10(14Q11.2) MUTATED   22  3
  AMP PEAK 10(14Q11.2) WILD-TYPE 47 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(14Q11.2) MUTATED     22    3
  AMP PEAK 10(14Q11.2) WILD-TYPE   47   15
     clus
vv    AMP PEAK 10(14Q11.2) MUTATED AMP PEAK 10(14Q11.2) WILD-TYPE
  NO                            22                             47
  YES                            3                             15
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AMP PEAK 10(14Q11.2) MUTATED                                       0
  AMP PEAK 10(14Q11.2) WILD-TYPE                                     1
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AMP PEAK 10(14Q11.2) MUTATED                                          0
  AMP PEAK 10(14Q11.2) WILD-TYPE                                        4
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AMP PEAK 10(14Q11.2) MUTATED                                     27
  AMP PEAK 10(14Q11.2) WILD-TYPE                                   58
D10V8, multiclass
                                          clus
vv                                         AMP PEAK 10(14Q11.2) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               27
                                          clus
vv                                         AMP PEAK 10(14Q11.2) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 10(14Q11.2) MUTATED   17  4  3  1
  AMP PEAK 10(14Q11.2) WILD-TYPE 46  3  9  4
D10V9, multiclass
    clus
vv   AMP PEAK 10(14Q11.2) MUTATED AMP PEAK 10(14Q11.2) WILD-TYPE
  R0                           17                             46
  R1                            4                              3
  R2                            3                              9
  RX                            1                              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"
D10V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(14Q11.2) MUTATED       1                         0    22
  AMP PEAK 10(14Q11.2) WILD-TYPE     1                         1    54
D10V11, multiclass
                           clus
vv                          AMP PEAK 10(14Q11.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               22
                           clus
vv                          AMP PEAK 10(14Q11.2) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
                                cls
clus                              0  1
  AMP PEAK 10(14Q11.2) MUTATED    4 11
  AMP PEAK 10(14Q11.2) WILD-TYPE  4 27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(14Q11.2) MUTATED      4   11
  AMP PEAK 10(14Q11.2) WILD-TYPE    4   27
                        clus
vv                       AMP PEAK 10(14Q11.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           11
                        clus
vv                       AMP PEAK 10(14Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             27
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(16P13.3) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 11(16P13.3) MUTATED   36 14
  AMP PEAK 11(16P13.3) WILD-TYPE 21 19
  AMP PEAK 11(16P13.3) MUTATED AMP PEAK 11(16P13.3) WILD-TYPE 
                            50                             40 
  AMP PEAK 11(16P13.3) MUTATED AMP PEAK 11(16P13.3) WILD-TYPE 
                            14                             19 
$`AMP PEAK 11(16P13.3) MUTATED`
TCGA-OR-A5L5 TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J9 
       43.30        44.55        68.75        13.91        12.00        44.45 
TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
       30.31        57.53        66.25        17.79        69.37        76.64 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       16.11        49.22        67.59        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 
       66.51        31.23        27.02       108.13       113.92        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW 
       16.37        24.62        46.49        83.80       153.63        68.25 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 
       12.85         4.11        58.55        31.79        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LL 
       28.64        23.64         5.23        39.35        14.63        53.03 
TCGA-OR-A5LM TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       61.08        61.05        28.04        36.03        18.05        38.50 
TCGA-PA-A5YG TCGA-PK-A5HC 
       24.85        22.32 

$`AMP PEAK 11(16P13.3) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J2 
       33.83        91.30        39.58        12.59        42.51        55.13 
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE 
       88.87        16.11        19.04        18.12        99.88        69.21 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW 
       18.48        39.25        15.25        12.59         9.50        72.39 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KQ 
       18.15        32.68        49.08        11.31        24.36        88.01 
TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5LE 
       95.18       127.50        44.84        60.89       152.15        21.76 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LN 
       52.24        78.41        14.33        36.33        90.08        77.00 
TCGA-OR-A5LO TCGA-P6-A5OH TCGA-PK-A5H9 TCGA-PK-A5HA 
       79.07         0.00        20.25        39.48 

  AMP PEAK 11(16P13.3) MUTATED AMP PEAK 11(16P13.3) WILD-TYPE 
                          4.11                           0.00 
  AMP PEAK 11(16P13.3) MUTATED AMP PEAK 11(16P13.3) WILD-TYPE 
                        153.63                         152.15 
  AMP PEAK 11(16P13.3) MUTATED AMP PEAK 11(16P13.3) WILD-TYPE 
                        36.145                         39.530 
[1] "4.1 - 153.6 (36.1)" "0.0 - 152.2 (39.5)"
[1] "hr=" "1.6"
D11V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 11(16P13.3) MUTATED         4       25        11        9
  AMP PEAK 11(16P13.3) WILD-TYPE       5       18         7        9
D11V3, multiclass
           clus
vv          AMP PEAK 11(16P13.3) MUTATED AMP PEAK 11(16P13.3) WILD-TYPE
  STAGE I                              4                              5
  STAGE II                            25                             18
  STAGE III                           11                              7
  STAGE IV                             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"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 11(16P13.3) MUTATED    4 27  6 12
  AMP PEAK 11(16P13.3) WILD-TYPE  5 21  5  8
D11V4, multiclass
    clus
vv   AMP PEAK 11(16P13.3) MUTATED AMP PEAK 11(16P13.3) WILD-TYPE
  T1                            4                              5
  T2                           27                             21
  T3                            6                              5
  T4                           12                              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"
D11V5, binary
                                cls
clus                              0  1
  AMP PEAK 11(16P13.3) MUTATED   43  6
  AMP PEAK 11(16P13.3) WILD-TYPE 35  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(16P13.3) MUTATED     43    6
  AMP PEAK 11(16P13.3) WILD-TYPE   35    4
   clus
vv  AMP PEAK 11(16P13.3) MUTATED AMP PEAK 11(16P13.3) WILD-TYPE
  0                           43                             35
  1                            6                              4
[1] 2 2
[1] FALSE
D11V6, binary
                                cls
clus                              0  1
  AMP PEAK 11(16P13.3) MUTATED   29 21
  AMP PEAK 11(16P13.3) WILD-TYPE 30 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(16P13.3) MUTATED     29   21
  AMP PEAK 11(16P13.3) WILD-TYPE   30   10
        clus
vv       AMP PEAK 11(16P13.3) MUTATED AMP PEAK 11(16P13.3) WILD-TYPE
  FEMALE                           29                             30
  MALE                             21                             10
[1] 2 2
[1] FALSE
D11V7, binary
                                cls
clus                              0  1
  AMP PEAK 11(16P13.3) MUTATED   40  8
  AMP PEAK 11(16P13.3) WILD-TYPE 29 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(16P13.3) MUTATED     40    8
  AMP PEAK 11(16P13.3) WILD-TYPE   29   10
     clus
vv    AMP PEAK 11(16P13.3) MUTATED AMP PEAK 11(16P13.3) WILD-TYPE
  NO                            40                             29
  YES                            8                             10
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AMP PEAK 11(16P13.3) MUTATED                                       1
  AMP PEAK 11(16P13.3) WILD-TYPE                                     0
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AMP PEAK 11(16P13.3) MUTATED                                          2
  AMP PEAK 11(16P13.3) WILD-TYPE                                        2
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AMP PEAK 11(16P13.3) MUTATED                                     47
  AMP PEAK 11(16P13.3) WILD-TYPE                                   38
D11V8, multiclass
                                          clus
vv                                         AMP PEAK 11(16P13.3) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               47
                                          clus
vv                                         AMP PEAK 11(16P13.3) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 11(16P13.3) MUTATED   34  4  6  4
  AMP PEAK 11(16P13.3) WILD-TYPE 29  3  6  1
D11V9, multiclass
    clus
vv   AMP PEAK 11(16P13.3) MUTATED AMP PEAK 11(16P13.3) WILD-TYPE
  R0                           34                             29
  R1                            4                              3
  R2                            6                              6
  RX                            4                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(16P13.3) MUTATED       1                         0    43
  AMP PEAK 11(16P13.3) WILD-TYPE     1                         1    33
D11V11, multiclass
                           clus
vv                          AMP PEAK 11(16P13.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               43
                           clus
vv                          AMP PEAK 11(16P13.3) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, binary
                                cls
clus                              0  1
  AMP PEAK 11(16P13.3) MUTATED    4 20
  AMP PEAK 11(16P13.3) WILD-TYPE  4 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(16P13.3) MUTATED      4   20
  AMP PEAK 11(16P13.3) WILD-TYPE    4   18
                        clus
vv                       AMP PEAK 11(16P13.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           20
                        clus
vv                       AMP PEAK 11(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             18
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(16Q22.1) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 12(16Q22.1) MUTATED   37 19
  AMP PEAK 12(16Q22.1) WILD-TYPE 20 14
  AMP PEAK 12(16Q22.1) MUTATED AMP PEAK 12(16Q22.1) WILD-TYPE 
                            56                             34 
  AMP PEAK 12(16Q22.1) MUTATED AMP PEAK 12(16Q22.1) WILD-TYPE 
                            19                             14 
$`AMP PEAK 12(16Q22.1) MUTATED`
TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 
       43.30        12.59        68.75        13.91        12.00        16.11 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       44.45        30.31        57.53        69.21        66.25        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ 
       69.37        76.64        16.11        49.22        15.25        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
      121.25        29.82        66.51        31.23        27.02       108.13 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU 
      113.92        35.57        24.62        46.49        83.80       153.63 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
       68.25        44.84        12.85         4.11        58.55        60.89 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       31.79        28.31        29.10        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LM 
       39.35        14.63        52.24        14.33        53.03        61.08 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       79.07        61.05        28.04        36.03        18.05        38.50 
TCGA-P6-A5OH TCGA-PA-A5YG 
        0.00        24.85 

$`AMP PEAK 12(16Q22.1) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       33.83        91.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JL TCGA-OR-A5JM 
       88.87        19.04        18.12        99.88        67.59        18.48 
TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K2 
       39.25        12.59         9.50        72.39        18.15        32.68 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KQ TCGA-OR-A5KT 
       16.37        49.08        11.31        24.36        88.01        95.18 
TCGA-OR-A5KV TCGA-OR-A5L3 TCGA-OR-A5LE TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
      127.50       152.15        21.76        78.41        36.33        90.08 
TCGA-OR-A5LN TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       77.00        20.25        39.48        22.32 

  AMP PEAK 12(16Q22.1) MUTATED AMP PEAK 12(16Q22.1) WILD-TYPE 
                           0.0                            9.5 
  AMP PEAK 12(16Q22.1) MUTATED AMP PEAK 12(16Q22.1) WILD-TYPE 
                        153.63                         152.15 
  AMP PEAK 12(16Q22.1) MUTATED AMP PEAK 12(16Q22.1) WILD-TYPE 
                        36.145                         39.530 
[1] "0.0 - 153.6 (36.1)" "9.5 - 152.2 (39.5)"
[1] "hr=" "1"  
D12V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 12(16Q22.1) MUTATED         4       27        12       12
  AMP PEAK 12(16Q22.1) WILD-TYPE       5       16         6        6
D12V3, multiclass
           clus
vv          AMP PEAK 12(16Q22.1) MUTATED AMP PEAK 12(16Q22.1) WILD-TYPE
  STAGE I                              4                              5
  STAGE II                            27                             16
  STAGE III                           12                              6
  STAGE IV                            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"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 12(16Q22.1) MUTATED    4 30  7 14
  AMP PEAK 12(16Q22.1) WILD-TYPE  5 18  4  6
D12V4, multiclass
    clus
vv   AMP PEAK 12(16Q22.1) MUTATED AMP PEAK 12(16Q22.1) WILD-TYPE
  T1                            4                              5
  T2                           30                             18
  T3                            7                              4
  T4                           14                              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"
D12V5, binary
                                cls
clus                              0  1
  AMP PEAK 12(16Q22.1) MUTATED   48  7
  AMP PEAK 12(16Q22.1) WILD-TYPE 30  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(16Q22.1) MUTATED     48    7
  AMP PEAK 12(16Q22.1) WILD-TYPE   30    3
   clus
vv  AMP PEAK 12(16Q22.1) MUTATED AMP PEAK 12(16Q22.1) WILD-TYPE
  0                           48                             30
  1                            7                              3
[1] 2 2
[1] FALSE
D12V6, binary
                                cls
clus                              0  1
  AMP PEAK 12(16Q22.1) MUTATED   34 22
  AMP PEAK 12(16Q22.1) WILD-TYPE 25  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(16Q22.1) MUTATED     34   22
  AMP PEAK 12(16Q22.1) WILD-TYPE   25    9
        clus
vv       AMP PEAK 12(16Q22.1) MUTATED AMP PEAK 12(16Q22.1) WILD-TYPE
  FEMALE                           34                             25
  MALE                             22                              9
[1] 2 2
[1] FALSE
D12V7, binary
                                cls
clus                              0  1
  AMP PEAK 12(16Q22.1) MUTATED   47  7
  AMP PEAK 12(16Q22.1) WILD-TYPE 22 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(16Q22.1) MUTATED     47    7
  AMP PEAK 12(16Q22.1) WILD-TYPE   22   11
     clus
vv    AMP PEAK 12(16Q22.1) MUTATED AMP PEAK 12(16Q22.1) WILD-TYPE
  NO                            47                             22
  YES                            7                             11
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AMP PEAK 12(16Q22.1) MUTATED                                       1
  AMP PEAK 12(16Q22.1) WILD-TYPE                                     0
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AMP PEAK 12(16Q22.1) MUTATED                                          2
  AMP PEAK 12(16Q22.1) WILD-TYPE                                        2
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AMP PEAK 12(16Q22.1) MUTATED                                     53
  AMP PEAK 12(16Q22.1) WILD-TYPE                                   32
D12V8, multiclass
                                          clus
vv                                         AMP PEAK 12(16Q22.1) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               53
                                          clus
vv                                         AMP PEAK 12(16Q22.1) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 12(16Q22.1) MUTATED   36  4  9  5
  AMP PEAK 12(16Q22.1) WILD-TYPE 27  3  3  0
D12V9, multiclass
    clus
vv   AMP PEAK 12(16Q22.1) MUTATED AMP PEAK 12(16Q22.1) WILD-TYPE
  R0                           36                             27
  R1                            4                              3
  R2                            9                              3
  RX                            5                              0
[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"
D12V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(16Q22.1) MUTATED       0                         0    49
  AMP PEAK 12(16Q22.1) WILD-TYPE     2                         1    27
D12V11, multiclass
                           clus
vv                          AMP PEAK 12(16Q22.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               49
                           clus
vv                          AMP PEAK 12(16Q22.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, binary
                                cls
clus                              0  1
  AMP PEAK 12(16Q22.1) MUTATED    5 25
  AMP PEAK 12(16Q22.1) WILD-TYPE  3 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(16Q22.1) MUTATED      5   25
  AMP PEAK 12(16Q22.1) WILD-TYPE    3   13
                        clus
vv                       AMP PEAK 12(16Q22.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           25
                        clus
vv                       AMP PEAK 12(16Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             13
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(16Q24.2) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 13(16Q24.2) MUTATED   35 14
  AMP PEAK 13(16Q24.2) WILD-TYPE 22 19
  AMP PEAK 13(16Q24.2) MUTATED AMP PEAK 13(16Q24.2) WILD-TYPE 
                            49                             41 
  AMP PEAK 13(16Q24.2) MUTATED AMP PEAK 13(16Q24.2) WILD-TYPE 
                            14                             19 
$`AMP PEAK 13(16Q24.2) MUTATED`
TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J9 
       43.30        12.59        44.55        68.75        12.00        44.45 
TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH 
       30.31        57.53        69.21        66.25        17.79        69.37 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       76.64        16.11        49.22        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 
       66.51        31.23        27.02       108.13       113.92        35.57 
TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KY 
       24.62        46.49        83.80       153.63        68.25        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
        4.11        58.55        31.79        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO 
       23.64         5.23        14.63        53.03        61.08        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PA-A5YG 
       61.05        28.04        36.03        18.05        38.50        24.85 
TCGA-PK-A5HC 
       22.32 

$`AMP PEAK 13(16Q24.2) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J2 TCGA-OR-A5J4 
       33.83        91.30        39.58        42.51        55.13        13.91 
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JL 
       88.87        16.11        19.04        18.12        99.88        67.59 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW 
       18.48        39.25        15.25        12.59         9.50        72.39 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB 
       18.15        32.68        16.37        49.08        11.31        24.36 
TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5L2 TCGA-OR-A5L3 
       88.01        95.18       127.50        44.84        60.89       152.15 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ 
       39.35        21.76        52.24        78.41        14.33        36.33 
TCGA-OR-A5LK TCGA-OR-A5LN TCGA-P6-A5OH TCGA-PK-A5H9 TCGA-PK-A5HA 
       90.08        77.00         0.00        20.25        39.48 

  AMP PEAK 13(16Q24.2) MUTATED AMP PEAK 13(16Q24.2) WILD-TYPE 
                          4.11                           0.00 
  AMP PEAK 13(16Q24.2) MUTATED AMP PEAK 13(16Q24.2) WILD-TYPE 
                        153.63                         152.15 
  AMP PEAK 13(16Q24.2) MUTATED AMP PEAK 13(16Q24.2) WILD-TYPE 
                         36.26                          39.35 
[1] "4.1 - 153.6 (36.3)" "0.0 - 152.2 (39.4)"
[1] "hr=" "1.6"
D13V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 13(16Q24.2) MUTATED         4       26         9        9
  AMP PEAK 13(16Q24.2) WILD-TYPE       5       17         9        9
D13V3, multiclass
           clus
vv          AMP PEAK 13(16Q24.2) MUTATED AMP PEAK 13(16Q24.2) WILD-TYPE
  STAGE I                              4                              5
  STAGE II                            26                             17
  STAGE III                            9                              9
  STAGE IV                             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"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 13(16Q24.2) MUTATED    4 28  4 12
  AMP PEAK 13(16Q24.2) WILD-TYPE  5 20  7  8
D13V4, multiclass
    clus
vv   AMP PEAK 13(16Q24.2) MUTATED AMP PEAK 13(16Q24.2) WILD-TYPE
  T1                            4                              5
  T2                           28                             20
  T3                            4                              7
  T4                           12                              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"
D13V5, binary
                                cls
clus                              0  1
  AMP PEAK 13(16Q24.2) MUTATED   43  5
  AMP PEAK 13(16Q24.2) WILD-TYPE 35  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(16Q24.2) MUTATED     43    5
  AMP PEAK 13(16Q24.2) WILD-TYPE   35    5
   clus
vv  AMP PEAK 13(16Q24.2) MUTATED AMP PEAK 13(16Q24.2) WILD-TYPE
  0                           43                             35
  1                            5                              5
[1] 2 2
[1] FALSE
D13V6, binary
                                cls
clus                              0  1
  AMP PEAK 13(16Q24.2) MUTATED   29 20
  AMP PEAK 13(16Q24.2) WILD-TYPE 30 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(16Q24.2) MUTATED     29   20
  AMP PEAK 13(16Q24.2) WILD-TYPE   30   11
        clus
vv       AMP PEAK 13(16Q24.2) MUTATED AMP PEAK 13(16Q24.2) WILD-TYPE
  FEMALE                           29                             30
  MALE                             20                             11
[1] 2 2
[1] FALSE
D13V7, binary
                                cls
clus                              0  1
  AMP PEAK 13(16Q24.2) MUTATED   40  7
  AMP PEAK 13(16Q24.2) WILD-TYPE 29 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(16Q24.2) MUTATED     40    7
  AMP PEAK 13(16Q24.2) WILD-TYPE   29   11
     clus
vv    AMP PEAK 13(16Q24.2) MUTATED AMP PEAK 13(16Q24.2) WILD-TYPE
  NO                            40                             29
  YES                            7                             11
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AMP PEAK 13(16Q24.2) MUTATED                                       1
  AMP PEAK 13(16Q24.2) WILD-TYPE                                     0
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AMP PEAK 13(16Q24.2) MUTATED                                          2
  AMP PEAK 13(16Q24.2) WILD-TYPE                                        2
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AMP PEAK 13(16Q24.2) MUTATED                                     46
  AMP PEAK 13(16Q24.2) WILD-TYPE                                   39
D13V8, multiclass
                                          clus
vv                                         AMP PEAK 13(16Q24.2) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               46
                                          clus
vv                                         AMP PEAK 13(16Q24.2) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 13(16Q24.2) MUTATED   34  4  6  3
  AMP PEAK 13(16Q24.2) WILD-TYPE 29  3  6  2
D13V9, multiclass
    clus
vv   AMP PEAK 13(16Q24.2) MUTATED AMP PEAK 13(16Q24.2) WILD-TYPE
  R0                           34                             29
  R1                            4                              3
  R2                            6                              6
  RX                            3                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(16Q24.2) MUTATED       1                         0    41
  AMP PEAK 13(16Q24.2) WILD-TYPE     1                         1    35
D13V11, multiclass
                           clus
vv                          AMP PEAK 13(16Q24.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               41
                           clus
vv                          AMP PEAK 13(16Q24.2) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V12, binary
                                cls
clus                              0  1
  AMP PEAK 13(16Q24.2) MUTATED    3 20
  AMP PEAK 13(16Q24.2) WILD-TYPE  5 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(16Q24.2) MUTATED      3   20
  AMP PEAK 13(16Q24.2) WILD-TYPE    5   18
                        clus
vv                       AMP PEAK 13(16Q24.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           20
                        clus
vv                       AMP PEAK 13(16Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             18
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(17Q25.3) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 14(17Q25.3) MUTATED    9  9
  AMP PEAK 14(17Q25.3) WILD-TYPE 48 24
  AMP PEAK 14(17Q25.3) MUTATED AMP PEAK 14(17Q25.3) WILD-TYPE 
                            18                             72 
  AMP PEAK 14(17Q25.3) MUTATED AMP PEAK 14(17Q25.3) WILD-TYPE 
                             9                             24 
$`AMP PEAK 14(17Q25.3) MUTATED`
TCGA-OR-A5KP TCGA-OR-A5J8 TCGA-OR-A5JH TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JQ 
       91.30        19.04        69.37        18.48        15.25        36.26 
TCGA-OR-A5JY TCGA-OR-A5K6 TCGA-OR-A5KU TCGA-OR-A5L2 TCGA-OR-A5LD TCGA-OR-A5LF 
       18.15        49.08       153.63        60.89        39.35        14.63 
TCGA-OR-A5LI TCGA-OR-A5LO TCGA-OR-A5LT TCGA-P6-A5OH TCGA-PK-A5HA TCGA-PK-A5HC 
       14.33        79.07        18.05         0.00        39.48        22.32 

$`AMP PEAK 14(17Q25.3) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        43.30        39.58        12.59        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        68.75        13.91        12.00        88.87        16.11 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       44.45        30.31        18.12        57.53        99.88        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       66.25        17.79        76.64        16.11        49.22        67.59 
TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
       39.25       121.25        12.59        29.82         9.50        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       72.39        31.23        27.02       108.13        32.68       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       35.57        16.37        24.62        11.31        24.36        46.49 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       88.01        83.80        95.18       127.50        68.25        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
       12.85         4.11        58.55       152.15        31.79        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG 
       29.10        28.64        23.64         5.23        21.76        52.24 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       78.41        36.33        90.08        53.03        61.08        77.00 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5H9 
       61.05        28.04        36.03        38.50        24.85        20.25 

  AMP PEAK 14(17Q25.3) MUTATED AMP PEAK 14(17Q25.3) WILD-TYPE 
                          0.00                           4.11 
  AMP PEAK 14(17Q25.3) MUTATED AMP PEAK 14(17Q25.3) WILD-TYPE 
                        153.63                         152.15 
  AMP PEAK 14(17Q25.3) MUTATED AMP PEAK 14(17Q25.3) WILD-TYPE 
                        29.290                         39.415 
[1] "0.0 - 153.6 (29.3)" "4.1 - 152.2 (39.4)"
[1] "hr=" "1.7"
D14V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 14(17Q25.3) MUTATED         1        8         5        4
  AMP PEAK 14(17Q25.3) WILD-TYPE       8       35        13       14
D14V3, multiclass
           clus
vv          AMP PEAK 14(17Q25.3) MUTATED AMP PEAK 14(17Q25.3) WILD-TYPE
  STAGE I                              1                              8
  STAGE II                             8                             35
  STAGE III                            5                             13
  STAGE IV                             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"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 14(17Q25.3) MUTATED    1  8  3  6
  AMP PEAK 14(17Q25.3) WILD-TYPE  8 40  8 14
D14V4, multiclass
    clus
vv   AMP PEAK 14(17Q25.3) MUTATED AMP PEAK 14(17Q25.3) WILD-TYPE
  T1                            1                              8
  T2                            8                             40
  T3                            3                              8
  T4                            6                             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"
D14V5, binary
                                cls
clus                              0  1
  AMP PEAK 14(17Q25.3) MUTATED   17  1
  AMP PEAK 14(17Q25.3) WILD-TYPE 61  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(17Q25.3) MUTATED     17    1
  AMP PEAK 14(17Q25.3) WILD-TYPE   61    9
   clus
vv  AMP PEAK 14(17Q25.3) MUTATED AMP PEAK 14(17Q25.3) WILD-TYPE
  0                           17                             61
  1                            1                              9
[1] 2 2
[1] FALSE
D14V6, binary
                                cls
clus                              0  1
  AMP PEAK 14(17Q25.3) MUTATED   13  5
  AMP PEAK 14(17Q25.3) WILD-TYPE 46 26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(17Q25.3) MUTATED     13    5
  AMP PEAK 14(17Q25.3) WILD-TYPE   46   26
        clus
vv       AMP PEAK 14(17Q25.3) MUTATED AMP PEAK 14(17Q25.3) WILD-TYPE
  FEMALE                           13                             46
  MALE                              5                             26
[1] 2 2
[1] FALSE
D14V7, binary
                                cls
clus                              0  1
  AMP PEAK 14(17Q25.3) MUTATED   15  3
  AMP PEAK 14(17Q25.3) WILD-TYPE 54 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(17Q25.3) MUTATED     15    3
  AMP PEAK 14(17Q25.3) WILD-TYPE   54   15
     clus
vv    AMP PEAK 14(17Q25.3) MUTATED AMP PEAK 14(17Q25.3) WILD-TYPE
  NO                            15                             54
  YES                            3                             15
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AMP PEAK 14(17Q25.3) MUTATED                                       1
  AMP PEAK 14(17Q25.3) WILD-TYPE                                     0
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AMP PEAK 14(17Q25.3) MUTATED                                          1
  AMP PEAK 14(17Q25.3) WILD-TYPE                                        3
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AMP PEAK 14(17Q25.3) MUTATED                                     16
  AMP PEAK 14(17Q25.3) WILD-TYPE                                   69
D14V8, multiclass
                                          clus
vv                                         AMP PEAK 14(17Q25.3) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               16
                                          clus
vv                                         AMP PEAK 14(17Q25.3) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 14(17Q25.3) MUTATED   12  2  3  1
  AMP PEAK 14(17Q25.3) WILD-TYPE 51  5  9  4
D14V9, multiclass
    clus
vv   AMP PEAK 14(17Q25.3) MUTATED AMP PEAK 14(17Q25.3) WILD-TYPE
  R0                           12                             51
  R1                            2                              5
  R2                            3                              9
  RX                            1                              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"
D14V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(17Q25.3) MUTATED       1                         0    14
  AMP PEAK 14(17Q25.3) WILD-TYPE     1                         1    62
D14V11, multiclass
                           clus
vv                          AMP PEAK 14(17Q25.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               14
                           clus
vv                          AMP PEAK 14(17Q25.3) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, binary
                                cls
clus                              0  1
  AMP PEAK 14(17Q25.3) MUTATED    1  9
  AMP PEAK 14(17Q25.3) WILD-TYPE  7 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(17Q25.3) MUTATED      1    9
  AMP PEAK 14(17Q25.3) WILD-TYPE    7   29
                        clus
vv                       AMP PEAK 14(17Q25.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            9
                        clus
vv                       AMP PEAK 14(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                             29
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(19P13.12) MUTATION ANALYSIS
D15V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 15(19P13.12) MUTATED   33 25
  AMP PEAK 15(19P13.12) WILD-TYPE 24  8
  AMP PEAK 15(19P13.12) MUTATED AMP PEAK 15(19P13.12) WILD-TYPE 
                             58                              32 
  AMP PEAK 15(19P13.12) MUTATED AMP PEAK 15(19P13.12) WILD-TYPE 
                             25                               8 
$`AMP PEAK 15(19P13.12) MUTATED`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5LB TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 
       33.83        91.30        39.58        55.13        68.75        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC 
       12.00        88.87        16.11        44.45        30.31        57.53 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV 
       49.22        18.48        15.25        36.26       121.25        66.51 
TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 
       31.23        32.68       113.92        16.37        24.62        11.31 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       46.49        83.80       153.63        68.25        44.84        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LC 
        4.11        58.55        60.89        31.79        29.10         5.23 
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        90.08        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LS TCGA-OR-A5LT 
       61.08        77.00        79.07        61.05        36.03        18.05 
TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5HC 
       38.50         0.00        24.85        22.32 

$`AMP PEAK 15(19P13.12) WILD-TYPE`
TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J8 TCGA-OR-A5JB 
       43.30        12.59        42.51        44.55        19.04        18.12 
TCGA-OR-A5JD TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU 
       99.88        67.59        39.25        12.59        29.82         9.50 
TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K4 TCGA-OR-A5K6 
       72.39        18.15        27.02       108.13        35.57        49.08 
TCGA-OR-A5KB TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5L3 TCGA-OR-A5L6 
       24.36        88.01        95.18       127.50       152.15        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LR 
       28.64        23.64        21.76        52.24        14.33        28.04 
TCGA-PK-A5H9 TCGA-PK-A5HA 
       20.25        39.48 

  AMP PEAK 15(19P13.12) MUTATED AMP PEAK 15(19P13.12) WILD-TYPE 
                            0.0                             9.5 
  AMP PEAK 15(19P13.12) MUTATED AMP PEAK 15(19P13.12) WILD-TYPE 
                         153.63                          152.15 
  AMP PEAK 15(19P13.12) MUTATED AMP PEAK 15(19P13.12) WILD-TYPE 
                         39.465                          32.695 
[1] "0.0 - 153.6 (39.5)" "9.5 - 152.2 (32.7)"
[1] "hr=" "1.7"
D15V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 15(19P13.12) MUTATED         3       27        13       14
  AMP PEAK 15(19P13.12) WILD-TYPE       6       16         5        4
D15V3, multiclass
           clus
vv          AMP PEAK 15(19P13.12) MUTATED AMP PEAK 15(19P13.12) WILD-TYPE
  STAGE I                               3                               6
  STAGE II                             27                              16
  STAGE III                            13                               5
  STAGE IV                             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"
                                 vv
clus                              T1 T2 T3 T4
  AMP PEAK 15(19P13.12) MUTATED    3 31  8 15
  AMP PEAK 15(19P13.12) WILD-TYPE  6 17  3  5
D15V4, multiclass
    clus
vv   AMP PEAK 15(19P13.12) MUTATED AMP PEAK 15(19P13.12) WILD-TYPE
  T1                             3                               6
  T2                            31                              17
  T3                             8                               3
  T4                            15                               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"
D15V5, binary
                                 cls
clus                               0  1
  AMP PEAK 15(19P13.12) MUTATED   49  8
  AMP PEAK 15(19P13.12) WILD-TYPE 29  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 15(19P13.12) MUTATED     49    8
  AMP PEAK 15(19P13.12) WILD-TYPE   29    2
   clus
vv  AMP PEAK 15(19P13.12) MUTATED AMP PEAK 15(19P13.12) WILD-TYPE
  0                            49                              29
  1                             8                               2
[1] 2 2
[1] FALSE
D15V6, binary
                                 cls
clus                               0  1
  AMP PEAK 15(19P13.12) MUTATED   38 20
  AMP PEAK 15(19P13.12) WILD-TYPE 21 11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 15(19P13.12) MUTATED     38   20
  AMP PEAK 15(19P13.12) WILD-TYPE   21   11
        clus
vv       AMP PEAK 15(19P13.12) MUTATED AMP PEAK 15(19P13.12) WILD-TYPE
  FEMALE                            38                              21
  MALE                              20                              11
[1] 2 2
[1] FALSE
D15V7, binary
                                 cls
clus                               0  1
  AMP PEAK 15(19P13.12) MUTATED   48  8
  AMP PEAK 15(19P13.12) WILD-TYPE 21 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 15(19P13.12) MUTATED     48    8
  AMP PEAK 15(19P13.12) WILD-TYPE   21   10
     clus
vv    AMP PEAK 15(19P13.12) MUTATED AMP PEAK 15(19P13.12) WILD-TYPE
  NO                             48                              21
  YES                             8                              10
[1] 2 2
[1] FALSE
                                 vv
clus                              ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AMP PEAK 15(19P13.12) MUTATED                                       1
  AMP PEAK 15(19P13.12) WILD-TYPE                                     0
                                 vv
clus                              ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AMP PEAK 15(19P13.12) MUTATED                                          3
  AMP PEAK 15(19P13.12) WILD-TYPE                                        1
                                 vv
clus                              ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AMP PEAK 15(19P13.12) MUTATED                                     54
  AMP PEAK 15(19P13.12) WILD-TYPE                                   31
D15V8, multiclass
                                          clus
vv                                         AMP PEAK 15(19P13.12) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                             3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                54
                                          clus
vv                                         AMP PEAK 15(19P13.12) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                  0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                               1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                  31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 15(19P13.12) MUTATED   39  5  9  3
  AMP PEAK 15(19P13.12) WILD-TYPE 24  2  3  2
D15V9, multiclass
    clus
vv   AMP PEAK 15(19P13.12) MUTATED AMP PEAK 15(19P13.12) WILD-TYPE
  R0                            39                              24
  R1                             5                               2
  R2                             9                               3
  RX                             3                               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V10, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(19P13.12) MUTATED       1                         1    48
  AMP PEAK 15(19P13.12) WILD-TYPE     1                         0    28
D15V11, multiclass
                           clus
vv                          AMP PEAK 15(19P13.12) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                48
                           clus
vv                          AMP PEAK 15(19P13.12) WILD-TYPE
  ASIAN                                                   1
  BLACK OR AFRICAN AMERICAN                               0
  WHITE                                                  28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, binary
                                 cls
clus                               0  1
  AMP PEAK 15(19P13.12) MUTATED    7 23
  AMP PEAK 15(19P13.12) WILD-TYPE  1 15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 15(19P13.12) MUTATED      7   23
  AMP PEAK 15(19P13.12) WILD-TYPE    1   15
                        clus
vv                       AMP PEAK 15(19P13.12) MUTATED
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            23
                        clus
vv                       AMP PEAK 15(19P13.12) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                              15
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(19Q12) MUTATION ANALYSIS
D16V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 16(19Q12) MUTATED   30 26
  AMP PEAK 16(19Q12) WILD-TYPE 27  7
  AMP PEAK 16(19Q12) MUTATED AMP PEAK 16(19Q12) WILD-TYPE 
                          56                           34 
  AMP PEAK 16(19Q12) MUTATED AMP PEAK 16(19Q12) WILD-TYPE 
                          26                            7 
$`AMP PEAK 16(19Q12) MUTATED`
TCGA-OR-A5KP TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 
       91.30        39.58        44.55        55.13        68.75        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC 
       12.00        88.87        16.11        44.45        30.31        57.53 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV 
       49.22        18.48        15.25        36.26       121.25        66.51 
TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 
       31.23        32.68       113.92        16.37        24.62        11.31 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
       46.49        83.80       153.63        44.84        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LC TCGA-OR-A5LD 
       58.55        60.89        31.79        29.10         5.23        39.35 
TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       78.41        14.33        36.33        90.08        53.03        61.08 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       79.07        61.05        36.03        18.05        38.50         0.00 
TCGA-PA-A5YG TCGA-PK-A5HC 
       24.85        22.32 

$`AMP PEAK 16(19Q12) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J8 TCGA-OR-A5JB 
       33.83        43.30        12.59        42.51        19.04        18.12 
TCGA-OR-A5JD TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU 
       99.88        67.59        39.25        12.59        29.82         9.50 
TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K4 TCGA-OR-A5K6 
       72.39        18.15        27.02       108.13        35.57        49.08 
TCGA-OR-A5KB TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5L3 
       24.36        88.01        95.18       127.50        68.25       152.15 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       28.31        28.64        23.64        21.76        14.63        52.24 
TCGA-OR-A5LN TCGA-OR-A5LR TCGA-PK-A5H9 TCGA-PK-A5HA 
       77.00        28.04        20.25        39.48 

  AMP PEAK 16(19Q12) MUTATED AMP PEAK 16(19Q12) WILD-TYPE 
                         0.0                          9.5 
  AMP PEAK 16(19Q12) MUTATED AMP PEAK 16(19Q12) WILD-TYPE 
                      153.63                       152.15 
  AMP PEAK 16(19Q12) MUTATED AMP PEAK 16(19Q12) WILD-TYPE 
                      39.465                       34.700 
[1] "0.0 - 153.6 (39.5)" "9.5 - 152.2 (34.7)"
[1] "hr=" "2.2"
D16V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 16(19Q12) MUTATED         3       26        11       15
  AMP PEAK 16(19Q12) WILD-TYPE       6       17         7        3
D16V3, multiclass
           clus
vv          AMP PEAK 16(19Q12) MUTATED AMP PEAK 16(19Q12) WILD-TYPE
  STAGE I                            3                            6
  STAGE II                          26                           17
  STAGE III                         11                            7
  STAGE IV                          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"
                              vv
clus                           T1 T2 T3 T4
  AMP PEAK 16(19Q12) MUTATED    3 29  7 16
  AMP PEAK 16(19Q12) WILD-TYPE  6 19  4  4
D16V4, multiclass
    clus
vv   AMP PEAK 16(19Q12) MUTATED AMP PEAK 16(19Q12) WILD-TYPE
  T1                          3                            6
  T2                         29                           19
  T3                          7                            4
  T4                         16                            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(19Q12) MUTATED   48  7
  AMP PEAK 16(19Q12) WILD-TYPE 30  3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(19Q12) MUTATED     48    7
  AMP PEAK 16(19Q12) WILD-TYPE   30    3
   clus
vv  AMP PEAK 16(19Q12) MUTATED AMP PEAK 16(19Q12) WILD-TYPE
  0                         48                           30
  1                          7                            3
[1] 2 2
[1] FALSE
D16V6, binary
                              cls
clus                            0  1
  AMP PEAK 16(19Q12) MUTATED   35 21
  AMP PEAK 16(19Q12) WILD-TYPE 24 10
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(19Q12) MUTATED     35   21
  AMP PEAK 16(19Q12) WILD-TYPE   24   10
        clus
vv       AMP PEAK 16(19Q12) MUTATED AMP PEAK 16(19Q12) WILD-TYPE
  FEMALE                         35                           24
  MALE                           21                           10
[1] 2 2
[1] FALSE
D16V7, binary
                              cls
clus                            0  1
  AMP PEAK 16(19Q12) MUTATED   47  7
  AMP PEAK 16(19Q12) WILD-TYPE 22 11
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(19Q12) MUTATED     47    7
  AMP PEAK 16(19Q12) WILD-TYPE   22   11
     clus
vv    AMP PEAK 16(19Q12) MUTATED AMP PEAK 16(19Q12) WILD-TYPE
  NO                          47                           22
  YES                          7                           11
[1] 2 2
[1] FALSE
                              vv
clus                           ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AMP PEAK 16(19Q12) MUTATED                                       1
  AMP PEAK 16(19Q12) WILD-TYPE                                     0
                              vv
clus                           ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AMP PEAK 16(19Q12) MUTATED                                          3
  AMP PEAK 16(19Q12) WILD-TYPE                                        1
                              vv
clus                           ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AMP PEAK 16(19Q12) MUTATED                                     52
  AMP PEAK 16(19Q12) WILD-TYPE                                   33
D16V8, multiclass
                                          clus
vv                                         AMP PEAK 16(19Q12) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                             1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                          3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                             52
                                          clus
vv                                         AMP PEAK 16(19Q12) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           R0 R1 R2 RX
  AMP PEAK 16(19Q12) MUTATED   36  5 10  3
  AMP PEAK 16(19Q12) WILD-TYPE 27  2  2  2
D16V9, multiclass
    clus
vv   AMP PEAK 16(19Q12) MUTATED AMP PEAK 16(19Q12) WILD-TYPE
  R0                         36                           27
  R1                          5                            2
  R2                         10                            2
  RX                          3                            2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V10, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(19Q12) MUTATED       1                         1    47
  AMP PEAK 16(19Q12) WILD-TYPE     1                         0    29
D16V11, multiclass
                           clus
vv                          AMP PEAK 16(19Q12) MUTATED
  ASIAN                                              1
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             47
                           clus
vv                          AMP PEAK 16(19Q12) WILD-TYPE
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V12, binary
                              cls
clus                            0  1
  AMP PEAK 16(19Q12) MUTATED    7 22
  AMP PEAK 16(19Q12) WILD-TYPE  1 16
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(19Q12) MUTATED      7   22
  AMP PEAK 16(19Q12) WILD-TYPE    1   16
                        clus
vv                       AMP PEAK 16(19Q12) MUTATED
  HISPANIC OR LATINO                              7
  NOT HISPANIC OR LATINO                         22
                        clus
vv                       AMP PEAK 16(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           16
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(XP11.22) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 17(XP11.22) MUTATED   31 18
  AMP PEAK 17(XP11.22) WILD-TYPE 26 15
  AMP PEAK 17(XP11.22) MUTATED AMP PEAK 17(XP11.22) WILD-TYPE 
                            49                             41 
  AMP PEAK 17(XP11.22) MUTATED AMP PEAK 17(XP11.22) WILD-TYPE 
                            18                             15 
$`AMP PEAK 17(XP11.22) MUTATED`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 
       33.83        43.30        39.58        55.13        68.75        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA 
       12.00        88.87        16.11        19.04        44.45        30.31 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JR TCGA-OR-A5JT 
       69.21        66.25        16.11        67.59       121.25        29.82 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K8 
       18.15        27.02       108.13       113.92        35.57        24.62 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       24.36        46.49        83.80       153.63       127.50        68.25 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L8 
       12.85         4.11        58.55        60.89        31.79        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ 
       28.64        23.64        39.35        14.63        78.41        36.33 
TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-PA-A5YG 
       61.08        79.07        61.05        28.04        18.05        24.85 
TCGA-PK-A5HC 
       22.32 

$`AMP PEAK 17(XP11.22) WILD-TYPE`
TCGA-OR-A5KP TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5JB TCGA-OR-A5JC 
       91.30        12.59        42.51        44.55        18.12        57.53 
TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JM 
       99.88        17.79        69.37        76.64        49.22        18.48 
TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JV 
       39.25        15.25        36.26        12.59         9.50        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
       72.39        31.23        32.68        16.37        49.08        11.31 
TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L6 TCGA-OR-A5LC 
       88.01        95.18        44.84       152.15        28.31         5.23 
TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN 
       21.76        52.24        14.33        90.08        53.03        77.00 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PK-A5H9 TCGA-PK-A5HA 
       36.03        38.50         0.00        20.25        39.48 

  AMP PEAK 17(XP11.22) MUTATED AMP PEAK 17(XP11.22) WILD-TYPE 
                          4.11                           0.00 
  AMP PEAK 17(XP11.22) MUTATED AMP PEAK 17(XP11.22) WILD-TYPE 
                        153.63                         152.15 
  AMP PEAK 17(XP11.22) MUTATED AMP PEAK 17(XP11.22) WILD-TYPE 
                         36.33                          39.25 
[1] "4.1 - 153.6 (36.3)" "0.0 - 152.2 (39.2)"
[1] "hr=" "1.1"
D17V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 17(XP11.22) MUTATED         4       24        12        9
  AMP PEAK 17(XP11.22) WILD-TYPE       5       19         6        9
D17V3, multiclass
           clus
vv          AMP PEAK 17(XP11.22) MUTATED AMP PEAK 17(XP11.22) WILD-TYPE
  STAGE I                              4                              5
  STAGE II                            24                             19
  STAGE III                           12                              6
  STAGE IV                             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"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 17(XP11.22) MUTATED    4 27  7 11
  AMP PEAK 17(XP11.22) WILD-TYPE  5 21  4  9
D17V4, multiclass
    clus
vv   AMP PEAK 17(XP11.22) MUTATED AMP PEAK 17(XP11.22) WILD-TYPE
  T1                            4                              5
  T2                           27                             21
  T3                            7                              4
  T4                           11                              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"
D17V5, binary
                                cls
clus                              0  1
  AMP PEAK 17(XP11.22) MUTATED   42  7
  AMP PEAK 17(XP11.22) WILD-TYPE 36  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(XP11.22) MUTATED     42    7
  AMP PEAK 17(XP11.22) WILD-TYPE   36    3
   clus
vv  AMP PEAK 17(XP11.22) MUTATED AMP PEAK 17(XP11.22) WILD-TYPE
  0                           42                             36
  1                            7                              3
[1] 2 2
[1] FALSE
D17V6, binary
                                cls
clus                              0  1
  AMP PEAK 17(XP11.22) MUTATED   34 15
  AMP PEAK 17(XP11.22) WILD-TYPE 25 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(XP11.22) MUTATED     34   15
  AMP PEAK 17(XP11.22) WILD-TYPE   25   16
        clus
vv       AMP PEAK 17(XP11.22) MUTATED AMP PEAK 17(XP11.22) WILD-TYPE
  FEMALE                           34                             25
  MALE                             15                             16
[1] 2 2
[1] FALSE
D17V7, binary
                                cls
clus                              0  1
  AMP PEAK 17(XP11.22) MUTATED   40  9
  AMP PEAK 17(XP11.22) WILD-TYPE 29  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(XP11.22) MUTATED     40    9
  AMP PEAK 17(XP11.22) WILD-TYPE   29    9
     clus
vv    AMP PEAK 17(XP11.22) MUTATED AMP PEAK 17(XP11.22) WILD-TYPE
  NO                            40                             29
  YES                            9                              9
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AMP PEAK 17(XP11.22) MUTATED                                       0
  AMP PEAK 17(XP11.22) WILD-TYPE                                     1
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AMP PEAK 17(XP11.22) MUTATED                                          1
  AMP PEAK 17(XP11.22) WILD-TYPE                                        3
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AMP PEAK 17(XP11.22) MUTATED                                     48
  AMP PEAK 17(XP11.22) WILD-TYPE                                   37
D17V8, multiclass
                                          clus
vv                                         AMP PEAK 17(XP11.22) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               48
                                          clus
vv                                         AMP PEAK 17(XP11.22) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 17(XP11.22) MUTATED   34  4  7  4
  AMP PEAK 17(XP11.22) WILD-TYPE 29  3  5  1
D17V9, multiclass
    clus
vv   AMP PEAK 17(XP11.22) MUTATED AMP PEAK 17(XP11.22) WILD-TYPE
  R0                           34                             29
  R1                            4                              3
  R2                            7                              5
  RX                            4                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(XP11.22) MUTATED       1                         1    42
  AMP PEAK 17(XP11.22) WILD-TYPE     1                         0    34
D17V11, multiclass
                           clus
vv                          AMP PEAK 17(XP11.22) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               42
                           clus
vv                          AMP PEAK 17(XP11.22) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, binary
                                cls
clus                              0  1
  AMP PEAK 17(XP11.22) MUTATED    8 23
  AMP PEAK 17(XP11.22) WILD-TYPE  0 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(XP11.22) MUTATED      8   23
  AMP PEAK 17(XP11.22) WILD-TYPE    0   15
                        clus
vv                       AMP PEAK 17(XP11.22) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           23
                        clus
vv                       AMP PEAK 17(XP11.22) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                             15
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(XQ28) MUTATION ANALYSIS
D18V1, survival
                             sevent
clus2                          0  1
  AMP PEAK 18(XQ28) MUTATED   31 15
  AMP PEAK 18(XQ28) WILD-TYPE 26 18
  AMP PEAK 18(XQ28) MUTATED AMP PEAK 18(XQ28) WILD-TYPE 
                         46                          44 
  AMP PEAK 18(XQ28) MUTATED AMP PEAK 18(XQ28) WILD-TYPE 
                         15                          18 
$`AMP PEAK 18(XQ28) MUTATED`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 
       43.30        39.58        42.51        55.13        68.75        12.00 
TCGA-OR-A5J6 TCGA-OR-A5J9 TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL 
       88.87        44.45        69.21        66.25        16.11        67.59 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 
      121.25        29.82        18.15        27.02       108.13       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS 
       35.57        16.37        24.62        24.36        46.49        83.80 
TCGA-OR-A5KU TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L4 
      153.63        44.84        12.85         4.11        58.55        31.79 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH 
       29.10        28.64        23.64        39.35        14.63        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        90.08        61.08        79.07        61.05        28.04 
TCGA-OR-A5LT TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5HC 
       18.05         0.00        24.85        22.32 

$`AMP PEAK 18(XQ28) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-P6-A5OG TCGA-OR-A5J1 TCGA-OR-A5J4 TCGA-OR-A5J7 
       33.83        91.30        12.59        44.55        13.91        16.11 
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG 
       19.04        30.31        18.12        57.53        99.88        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       69.37        76.64        49.22        18.48        39.25        15.25 
TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       36.26        12.59         9.50        66.51        72.39        31.23 
TCGA-OR-A5K2 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV 
       32.68        49.08        11.31        88.01        95.18       127.50 
TCGA-OR-A5KW TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LE 
       68.25        60.89       152.15        28.31         5.23        21.76 
TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI 
       52.24        14.33        53.03        77.00        36.03        38.50 
TCGA-PK-A5H9 TCGA-PK-A5HA 
       20.25        39.48 

  AMP PEAK 18(XQ28) MUTATED AMP PEAK 18(XQ28) WILD-TYPE 
                       0.00                        5.23 
  AMP PEAK 18(XQ28) MUTATED AMP PEAK 18(XQ28) WILD-TYPE 
                     153.63                      152.15 
  AMP PEAK 18(XQ28) MUTATED AMP PEAK 18(XQ28) WILD-TYPE 
                     39.465                      37.380 
[1] "0.0 - 153.6 (39.5)" "5.2 - 152.2 (37.4)"
[1] "hr=" "1.3"
D18V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 18(XQ28) MUTATED         4       23        10        8
  AMP PEAK 18(XQ28) WILD-TYPE       5       20         8       10
D18V3, multiclass
           clus
vv          AMP PEAK 18(XQ28) MUTATED AMP PEAK 18(XQ28) WILD-TYPE
  STAGE I                           4                           5
  STAGE II                         23                          20
  STAGE III                        10                           8
  STAGE IV                          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"
                             vv
clus                          T1 T2 T3 T4
  AMP PEAK 18(XQ28) MUTATED    4 25  5 11
  AMP PEAK 18(XQ28) WILD-TYPE  5 23  6  9
D18V4, multiclass
    clus
vv   AMP PEAK 18(XQ28) MUTATED AMP PEAK 18(XQ28) WILD-TYPE
  T1                         4                           5
  T2                        25                          23
  T3                         5                           6
  T4                        11                           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"
D18V5, binary
                             cls
clus                           0  1
  AMP PEAK 18(XQ28) MUTATED   40  5
  AMP PEAK 18(XQ28) WILD-TYPE 38  5
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 18(XQ28) MUTATED     40    5
  AMP PEAK 18(XQ28) WILD-TYPE   38    5
   clus
vv  AMP PEAK 18(XQ28) MUTATED AMP PEAK 18(XQ28) WILD-TYPE
  0                        40                          38
  1                         5                           5
[1] 2 2
[1] FALSE
D18V6, binary
                             cls
clus                           0  1
  AMP PEAK 18(XQ28) MUTATED   30 16
  AMP PEAK 18(XQ28) WILD-TYPE 29 15
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 18(XQ28) MUTATED     30   16
  AMP PEAK 18(XQ28) WILD-TYPE   29   15
        clus
vv       AMP PEAK 18(XQ28) MUTATED AMP PEAK 18(XQ28) WILD-TYPE
  FEMALE                        30                          29
  MALE                          16                          15
[1] 2 2
[1] FALSE
D18V7, binary
                             cls
clus                           0  1
  AMP PEAK 18(XQ28) MUTATED   38  8
  AMP PEAK 18(XQ28) WILD-TYPE 31 10
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 18(XQ28) MUTATED     38    8
  AMP PEAK 18(XQ28) WILD-TYPE   31   10
     clus
vv    AMP PEAK 18(XQ28) MUTATED AMP PEAK 18(XQ28) WILD-TYPE
  NO                         38                          31
  YES                         8                          10
[1] 2 2
[1] FALSE
                             vv
clus                          ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  AMP PEAK 18(XQ28) MUTATED                                       0
  AMP PEAK 18(XQ28) WILD-TYPE                                     1
                             vv
clus                          ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  AMP PEAK 18(XQ28) MUTATED                                          2
  AMP PEAK 18(XQ28) WILD-TYPE                                        2
                             vv
clus                          ADRENOCORTICAL CARCINOMA- USUAL TYPE
  AMP PEAK 18(XQ28) MUTATED                                     44
  AMP PEAK 18(XQ28) WILD-TYPE                                   41
D18V8, multiclass
                                          clus
vv                                         AMP PEAK 18(XQ28) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                            0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                         2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                            44
                                          clus
vv                                         AMP PEAK 18(XQ28) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                           2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          R0 R1 R2 RX
  AMP PEAK 18(XQ28) MUTATED   32  2  7  4
  AMP PEAK 18(XQ28) WILD-TYPE 31  5  5  1
D18V9, multiclass
    clus
vv   AMP PEAK 18(XQ28) MUTATED AMP PEAK 18(XQ28) WILD-TYPE
  R0                        32                          31
  R1                         2                           5
  R2                         7                           5
  RX                         4                           1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(XQ28) MUTATED       1                         1    37
  AMP PEAK 18(XQ28) WILD-TYPE     1                         0    39
D18V11, multiclass
                           clus
vv                          AMP PEAK 18(XQ28) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                            37
                           clus
vv                          AMP PEAK 18(XQ28) WILD-TYPE
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V12, binary
                             cls
clus                           0  1
  AMP PEAK 18(XQ28) MUTATED    5 22
  AMP PEAK 18(XQ28) WILD-TYPE  3 16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 18(XQ28) MUTATED      5   22
  AMP PEAK 18(XQ28) WILD-TYPE    3   16
                        clus
vv                       AMP PEAK 18(XQ28) MUTATED AMP PEAK 18(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             5                           3
  NOT HISPANIC OR LATINO                        22                          16
[1] 2 2
[1] FALSE

Clustering(19) Variable = DEL PEAK  1(1P36.23) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.23) MUTATED   22 16
  DEL PEAK  1(1P36.23) WILD-TYPE 35 17
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            38                             52 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            16                             17 
$`DEL PEAK  1(1P36.23) MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JD 
       55.13        13.91        16.11        44.45        57.53        99.88 
TCGA-OR-A5JE TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM 
       69.21        69.37        76.64        16.11        49.22        18.48 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       15.25        36.26        12.59        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KX 
       18.15        32.68        16.37        49.08        11.31        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LG 
        4.11        60.89       152.15        28.31         5.23        52.24 
TCGA-OR-A5LI TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       14.33        61.08        77.00        36.03        18.05        38.50 
TCGA-P6-A5OH TCGA-PK-A5HA 
        0.00        39.48 

$`DEL PEAK  1(1P36.23) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JA 
       44.55        68.75        12.00        88.87        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JR 
       18.12        66.25        17.79        67.59        39.25       121.25 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 
       29.82         9.50        27.02       108.13       113.92        35.57 
TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       24.62        24.36        46.49        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5L1 TCGA-OR-A5L4 
      153.63       127.50        68.25        12.85        58.55        31.79 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       29.10        28.64        23.64        39.35        21.76        14.63 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       78.41        36.33        90.08        53.03        79.07        61.05 
TCGA-OR-A5LR TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       28.04        24.85        20.25        22.32 

  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                           0.0                            9.5 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                        152.15                         153.63 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                         37.38                          39.30 
[1] "0.0 - 152.2 (37.4)" "9.5 - 153.6 (39.3)"
[1] "hr=" "1.6"
D19V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  1(1P36.23) MUTATED         4       16         7       10
  DEL PEAK  1(1P36.23) WILD-TYPE       5       27        11        8
D19V3, multiclass
           clus
vv          DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  STAGE I                              4                              5
  STAGE II                            16                             27
  STAGE III                            7                             11
  STAGE IV                            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"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK  1(1P36.23) MUTATED    4 18  7  8
  DEL PEAK  1(1P36.23) WILD-TYPE  5 30  4 12
D19V4, multiclass
    clus
vv   DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  T1                            4                              5
  T2                           18                             30
  T3                            7                              4
  T4                            8                             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"
D19V5, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED   32  5
  DEL PEAK  1(1P36.23) WILD-TYPE 46  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     32    5
  DEL PEAK  1(1P36.23) WILD-TYPE   46    5
   clus
vv  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  0                           32                             46
  1                            5                              5
[1] 2 2
[1] FALSE
D19V6, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED   24 14
  DEL PEAK  1(1P36.23) WILD-TYPE 35 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     24   14
  DEL PEAK  1(1P36.23) WILD-TYPE   35   17
        clus
vv       DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  FEMALE                           24                             35
  MALE                             14                             17
[1] 2 2
[1] FALSE
D19V7, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED   29  8
  DEL PEAK  1(1P36.23) WILD-TYPE 40 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     29    8
  DEL PEAK  1(1P36.23) WILD-TYPE   40   10
     clus
vv    DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  NO                            29                             40
  YES                            8                             10
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK  1(1P36.23) MUTATED                                       1
  DEL PEAK  1(1P36.23) WILD-TYPE                                     0
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK  1(1P36.23) MUTATED                                          2
  DEL PEAK  1(1P36.23) WILD-TYPE                                        2
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK  1(1P36.23) MUTATED                                     35
  DEL PEAK  1(1P36.23) WILD-TYPE                                   50
D19V8, multiclass
                                          clus
vv                                         DEL PEAK  1(1P36.23) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               35
                                          clus
vv                                         DEL PEAK  1(1P36.23) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK  1(1P36.23) MUTATED   24  2  8  2
  DEL PEAK  1(1P36.23) WILD-TYPE 39  5  4  3
D19V9, multiclass
    clus
vv   DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  R0                           24                             39
  R1                            2                              5
  R2                            8                              4
  RX                            2                              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"
D19V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.23) MUTATED       0                         0    33
  DEL PEAK  1(1P36.23) WILD-TYPE     2                         1    43
D19V11, multiclass
                           clus
vv                          DEL PEAK  1(1P36.23) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               33
                           clus
vv                          DEL PEAK  1(1P36.23) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.23) MUTATED    4 11
  DEL PEAK  1(1P36.23) WILD-TYPE  4 27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      4   11
  DEL PEAK  1(1P36.23) WILD-TYPE    4   27
                        clus
vv                       DEL PEAK  1(1P36.23) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           11
                        clus
vv                       DEL PEAK  1(1P36.23) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             27
[1] 2 2
[1] FALSE

Clustering(20) Variable = DEL PEAK  2(2Q22.1) MUTATION ANALYSIS
D20V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(2Q22.1) MUTATED   15  3
  DEL PEAK  2(2Q22.1) WILD-TYPE 42 30
  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                           18                            72 
  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                            3                            30 
$`DEL PEAK  2(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        99.88        69.37        49.22        67.59 
TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       36.26        12.59        66.51        72.39        31.23        18.15 
TCGA-OR-A5KB TCGA-OR-A5KU TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA 
       24.36       153.63        77.00        36.03        38.50        39.48 

$`DEL PEAK  2(2Q22.1) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF 
       16.11        19.04        44.45        18.12        69.21        66.25 
TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       17.79        76.64        16.11        18.48        39.25        15.25 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 
      121.25        29.82         9.50        27.02       108.13        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 
      113.92        35.57        16.37        49.08        24.62        11.31 
TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW 
       46.49        88.01        83.80        95.18       127.50        68.25 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       44.84        12.85         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
       31.79        28.31        29.10        28.64        23.64         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI 
       39.35        21.76        14.63        52.24        78.41        14.33 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP 
       36.33        90.08        53.03        61.08        79.07        61.05 
TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       28.04        18.05         0.00        24.85        20.25        22.32 

  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                        12.59                          0.00 
  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                       153.63                        152.15 
  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                        44.35                         35.95 
[1] "12.6 - 153.6 (44.3)" "0.0 - 152.2 (36.0)" 
[1] "hr=" "2.9"
D20V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  2(2Q22.1) MUTATED         2       10         1        4
  DEL PEAK  2(2Q22.1) WILD-TYPE       7       33        17       14
D20V3, multiclass
           clus
vv          DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE
  STAGE I                             2                             7
  STAGE II                           10                            33
  STAGE III                           1                            17
  STAGE IV                            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"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  2(2Q22.1) MUTATED    2 11  1  3
  DEL PEAK  2(2Q22.1) WILD-TYPE  7 37 10 17
D20V4, multiclass
    clus
vv   DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE
  T1                           2                             7
  T2                          11                            37
  T3                           1                            10
  T4                           3                            17
[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  2(2Q22.1) MUTATED   15  2
  DEL PEAK  2(2Q22.1) WILD-TYPE 63  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2Q22.1) MUTATED     15    2
  DEL PEAK  2(2Q22.1) WILD-TYPE   63    8
   clus
vv  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE
  0                          15                            63
  1                           2                             8
[1] 2 2
[1] FALSE
D20V6, binary
                               cls
clus                             0  1
  DEL PEAK  2(2Q22.1) MUTATED   12  6
  DEL PEAK  2(2Q22.1) WILD-TYPE 47 25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2Q22.1) MUTATED     12    6
  DEL PEAK  2(2Q22.1) WILD-TYPE   47   25
        clus
vv       DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE
  FEMALE                          12                            47
  MALE                             6                            25
[1] 2 2
[1] FALSE
D20V7, binary
                               cls
clus                             0  1
  DEL PEAK  2(2Q22.1) MUTATED   12  5
  DEL PEAK  2(2Q22.1) WILD-TYPE 57 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2Q22.1) MUTATED     12    5
  DEL PEAK  2(2Q22.1) WILD-TYPE   57   13
     clus
vv    DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE
  NO                           12                            57
  YES                           5                            13
[1] 2 2
[1] FALSE
                               vv
clus                            ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK  2(2Q22.1) MUTATED                                       1
  DEL PEAK  2(2Q22.1) WILD-TYPE                                     0
                               vv
clus                            ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK  2(2Q22.1) MUTATED                                          2
  DEL PEAK  2(2Q22.1) WILD-TYPE                                        2
                               vv
clus                            ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK  2(2Q22.1) MUTATED                                     15
  DEL PEAK  2(2Q22.1) WILD-TYPE                                   70
D20V8, multiclass
                                          clus
vv                                         DEL PEAK  2(2Q22.1) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                           2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                              15
                                          clus
vv                                         DEL PEAK  2(2Q22.1) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                             2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  2(2Q22.1) MUTATED   13  1  2  0
  DEL PEAK  2(2Q22.1) WILD-TYPE 50  6 10  5
D20V9, multiclass
    clus
vv   DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE
  R0                          13                            50
  R1                           1                             6
  R2                           2                            10
  RX                           0                             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"
D20V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(2Q22.1) MUTATED       0                         0    15
  DEL PEAK  2(2Q22.1) WILD-TYPE     2                         1    61
D20V11, multiclass
                           clus
vv                          DEL PEAK  2(2Q22.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              15
                           clus
vv                          DEL PEAK  2(2Q22.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V12, binary
                               cls
clus                             0  1
  DEL PEAK  2(2Q22.1) MUTATED    0  3
  DEL PEAK  2(2Q22.1) WILD-TYPE  8 35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(2Q22.1) MUTATED      0    3
  DEL PEAK  2(2Q22.1) WILD-TYPE    8   35
                        clus
vv                       DEL PEAK  2(2Q22.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           3
                        clus
vv                       DEL PEAK  2(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                            35
[1] 2 2
[1] FALSE

Clustering(21) Variable = DEL PEAK  3(2Q37.3) MUTATION ANALYSIS
D21V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  3(2Q37.3) MUTATED   15  6
  DEL PEAK  3(2Q37.3) WILD-TYPE 42 27
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           21                            69 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                            6                            27 
$`DEL PEAK  3(2Q37.3) MUTATED`
TCGA-OR-A5K0 TCGA-OR-A5LB TCGA-OR-A5J4 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC 
       33.83        39.58        13.91        44.45        30.31        57.53 
TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JS 
       99.88        69.37        49.22        67.59        36.26        12.59 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5L2 TCGA-OR-A5LC TCGA-OR-A5LN 
       66.51        72.39        31.23        60.89         5.23        77.00 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA 
       36.03        38.50        39.48 

$`DEL PEAK  3(2Q37.3) WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        12.59        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JB 
       68.75        12.00        88.87        16.11        19.04        18.12 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM 
       69.21        66.25        17.79        76.64        16.11        18.48 
TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JY 
       39.25        15.25       121.25        29.82         9.50        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       27.02       108.13        32.68       113.92        35.57        16.37 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ 
       49.08        24.62        11.31        24.36        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        68.25        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
       12.85         4.11        58.55       152.15        31.79        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       29.10        28.64        23.64        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       52.24        78.41        14.33        36.33        90.08        53.03 
TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OH 
       61.08        79.07        61.05        28.04        18.05         0.00 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       24.85        20.25        22.32 

  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                         5.23                          0.00 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                        99.88                        153.63 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                        39.58                         35.57 
[1] "5.2 - 99.9 (39.6)"  "0.0 - 153.6 (35.6)"
[1] "hr=" "1.4"
D21V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  3(2Q37.3) MUTATED         2       11         1        6
  DEL PEAK  3(2Q37.3) WILD-TYPE       7       32        17       12
D21V3, multiclass
           clus
vv          DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  STAGE I                             2                             7
  STAGE II                           11                            32
  STAGE III                           1                            17
  STAGE IV                            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"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  3(2Q37.3) MUTATED    2 12  2  4
  DEL PEAK  3(2Q37.3) WILD-TYPE  7 36  9 16
D21V4, multiclass
    clus
vv   DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  T1                           2                             7
  T2                          12                            36
  T3                           2                             9
  T4                           4                            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  3(2Q37.3) MUTATED   18  2
  DEL PEAK  3(2Q37.3) WILD-TYPE 60  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED     18    2
  DEL PEAK  3(2Q37.3) WILD-TYPE   60    8
   clus
vv  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  0                          18                            60
  1                           2                             8
[1] 2 2
[1] FALSE
D21V6, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q37.3) MUTATED   14  7
  DEL PEAK  3(2Q37.3) WILD-TYPE 45 24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED     14    7
  DEL PEAK  3(2Q37.3) WILD-TYPE   45   24
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  FEMALE                          14                            45
  MALE                             7                            24
[1] 2 2
[1] FALSE
D21V7, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q37.3) MUTATED   15  5
  DEL PEAK  3(2Q37.3) WILD-TYPE 54 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED     15    5
  DEL PEAK  3(2Q37.3) WILD-TYPE   54   13
     clus
vv    DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  NO                           15                            54
  YES                           5                            13
[1] 2 2
[1] FALSE
                               vv
clus                            ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK  3(2Q37.3) MUTATED                                       1
  DEL PEAK  3(2Q37.3) WILD-TYPE                                     0
                               vv
clus                            ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK  3(2Q37.3) MUTATED                                          2
  DEL PEAK  3(2Q37.3) WILD-TYPE                                        2
                               vv
clus                            ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK  3(2Q37.3) MUTATED                                     18
  DEL PEAK  3(2Q37.3) WILD-TYPE                                   67
D21V8, multiclass
                                          clus
vv                                         DEL PEAK  3(2Q37.3) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                           2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                              18
                                          clus
vv                                         DEL PEAK  3(2Q37.3) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                             2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  3(2Q37.3) MUTATED   15  1  3  0
  DEL PEAK  3(2Q37.3) WILD-TYPE 48  6  9  5
D21V9, multiclass
    clus
vv   DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  R0                          15                            48
  R1                           1                             6
  R2                           3                             9
  RX                           0                             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"
D21V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2Q37.3) MUTATED       0                         0    18
  DEL PEAK  3(2Q37.3) WILD-TYPE     2                         1    58
D21V11, multiclass
                           clus
vv                          DEL PEAK  3(2Q37.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              18
                           clus
vv                          DEL PEAK  3(2Q37.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, binary
                               cls
clus                             0  1
  DEL PEAK  3(2Q37.3) MUTATED    2  4
  DEL PEAK  3(2Q37.3) WILD-TYPE  6 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED      2    4
  DEL PEAK  3(2Q37.3) WILD-TYPE    6   34
                        clus
vv                       DEL PEAK  3(2Q37.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                           4
                        clus
vv                       DEL PEAK  3(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            34
[1] 2 2
[1] FALSE

Clustering(22) Variable = DEL PEAK  4(3Q13.31) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  4(3Q13.31) MUTATED   13 12
  DEL PEAK  4(3Q13.31) WILD-TYPE 44 21
  DEL PEAK  4(3Q13.31) MUTATED DEL PEAK  4(3Q13.31) WILD-TYPE 
                            25                             65 
  DEL PEAK  4(3Q13.31) MUTATED DEL PEAK  4(3Q13.31) WILD-TYPE 
                            12                             21 
$`DEL PEAK  4(3Q13.31) MUTATED`
TCGA-OR-A5KP TCGA-PK-A5HB TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       91.30        42.51        88.87        16.11        19.04        30.31 
TCGA-OR-A5JC TCGA-OR-A5JG TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JW 
       57.53        17.79        49.22        67.59        15.25        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KS TCGA-OR-A5L6 
       31.23        18.15        24.62        11.31        83.80        28.31 
TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LS 
        5.23        21.76        14.33        53.03        61.08        36.03 
TCGA-P6-A5OH 
        0.00 

$`DEL PEAK  4(3Q13.31) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J1 TCGA-OR-A5J2 
       33.83        43.30        39.58        12.59        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD 
       68.75        13.91        12.00        44.45        18.12        99.88 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM 
       69.21        66.25        69.37        76.64        16.11        18.48 
TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU 
       39.25        36.26       121.25        12.59        29.82         9.50 
TCGA-OR-A5JV TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
       66.51        27.02       108.13        32.68       113.92        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KT 
       16.37        49.08        24.36        46.49        88.01        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       127.50        68.25        44.84        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5L9 
       58.55        60.89       152.15        31.79        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
       23.64        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-A5LT 
       90.08        77.00        79.07        61.05        28.04        18.05 
TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       38.50        24.85        20.25        39.48        22.32 

  DEL PEAK  4(3Q13.31) MUTATED DEL PEAK  4(3Q13.31) WILD-TYPE 
                          0.00                           4.11 
  DEL PEAK  4(3Q13.31) MUTATED DEL PEAK  4(3Q13.31) WILD-TYPE 
                         91.30                         153.63 
  DEL PEAK  4(3Q13.31) MUTATED DEL PEAK  4(3Q13.31) WILD-TYPE 
                         30.31                          39.48 
[1] "0.0 - 91.3 (30.3)"  "4.1 - 153.6 (39.5)"
[1] "hr=" "1.8"
D22V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  4(3Q13.31) MUTATED         1       12         3        7
  DEL PEAK  4(3Q13.31) WILD-TYPE       8       31        15       11
D22V3, multiclass
           clus
vv          DEL PEAK  4(3Q13.31) MUTATED DEL PEAK  4(3Q13.31) WILD-TYPE
  STAGE I                              1                              8
  STAGE II                            12                             31
  STAGE III                            3                             15
  STAGE IV                             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"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK  4(3Q13.31) MUTATED    1 12  3  7
  DEL PEAK  4(3Q13.31) WILD-TYPE  8 36  8 13
D22V4, multiclass
    clus
vv   DEL PEAK  4(3Q13.31) MUTATED DEL PEAK  4(3Q13.31) WILD-TYPE
  T1                            1                              8
  T2                           12                             36
  T3                            3                              8
  T4                            7                             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"
D22V5, binary
                                cls
clus                              0  1
  DEL PEAK  4(3Q13.31) MUTATED   21  2
  DEL PEAK  4(3Q13.31) WILD-TYPE 57  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  4(3Q13.31) MUTATED     21    2
  DEL PEAK  4(3Q13.31) WILD-TYPE   57    8
   clus
vv  DEL PEAK  4(3Q13.31) MUTATED DEL PEAK  4(3Q13.31) WILD-TYPE
  0                           21                             57
  1                            2                              8
[1] 2 2
[1] FALSE
D22V6, binary
                                cls
clus                              0  1
  DEL PEAK  4(3Q13.31) MUTATED   12 13
  DEL PEAK  4(3Q13.31) WILD-TYPE 47 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  4(3Q13.31) MUTATED     12   13
  DEL PEAK  4(3Q13.31) WILD-TYPE   47   18
        clus
vv       DEL PEAK  4(3Q13.31) MUTATED DEL PEAK  4(3Q13.31) WILD-TYPE
  FEMALE                           12                             47
  MALE                             13                             18
[1] 2 2
[1] FALSE
D22V7, binary
                                cls
clus                              0  1
  DEL PEAK  4(3Q13.31) MUTATED   17  6
  DEL PEAK  4(3Q13.31) WILD-TYPE 52 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  4(3Q13.31) MUTATED     17    6
  DEL PEAK  4(3Q13.31) WILD-TYPE   52   12
     clus
vv    DEL PEAK  4(3Q13.31) MUTATED DEL PEAK  4(3Q13.31) WILD-TYPE
  NO                            17                             52
  YES                            6                             12
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK  4(3Q13.31) MUTATED                                       0
  DEL PEAK  4(3Q13.31) WILD-TYPE                                     1
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK  4(3Q13.31) MUTATED                                          0
  DEL PEAK  4(3Q13.31) WILD-TYPE                                        4
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK  4(3Q13.31) MUTATED                                     25
  DEL PEAK  4(3Q13.31) WILD-TYPE                                   60
D22V8, multiclass
                                          clus
vv                                         DEL PEAK  4(3Q13.31) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               25
                                          clus
vv                                         DEL PEAK  4(3Q13.31) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK  4(3Q13.31) MUTATED   15  3  5  0
  DEL PEAK  4(3Q13.31) WILD-TYPE 48  4  7  5
D22V9, multiclass
    clus
vv   DEL PEAK  4(3Q13.31) MUTATED DEL PEAK  4(3Q13.31) WILD-TYPE
  R0                           15                             48
  R1                            3                              4
  R2                            5                              7
  RX                            0                              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"
D22V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(3Q13.31) MUTATED       0                         1    20
  DEL PEAK  4(3Q13.31) WILD-TYPE     2                         0    56
D22V11, multiclass
                           clus
vv                          DEL PEAK  4(3Q13.31) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               20
                           clus
vv                          DEL PEAK  4(3Q13.31) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V12, binary
                                cls
clus                              0  1
  DEL PEAK  4(3Q13.31) MUTATED    3  8
  DEL PEAK  4(3Q13.31) WILD-TYPE  5 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  4(3Q13.31) MUTATED      3    8
  DEL PEAK  4(3Q13.31) WILD-TYPE    5   30
                        clus
vv                       DEL PEAK  4(3Q13.31) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                            8
                        clus
vv                       DEL PEAK  4(3Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             30
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK  5(4Q34.3) MUTATION ANALYSIS
D23V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(4Q34.3) MUTATED   12 13
  DEL PEAK  5(4Q34.3) WILD-TYPE 45 20
  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                           25                            65 
  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                           13                            20 
$`DEL PEAK  5(4Q34.3) MUTATED`
TCGA-PK-A5HB TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JK TCGA-OR-A5JM 
       42.51        13.91        16.11        18.12        49.22        18.48 
TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K6 
       15.25        12.59        66.51        18.15        32.68        49.08 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KS TCGA-OR-A5KY TCGA-OR-A5L2 
       24.62        11.31        24.36        83.80        12.85        60.89 
TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LI TCGA-OR-A5LS TCGA-P6-A5OH TCGA-PK-A5HA 
        5.23        21.76        14.33        36.03         0.00        39.48 
TCGA-PK-A5HC 
       22.32 

$`DEL PEAK  5(4Q34.3) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J1 
       33.83        91.30        43.30        39.58        12.59        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 
       55.13        68.75        12.00        88.87        19.04        44.45 
TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       30.31        57.53        99.88        69.21        66.25        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JQ 
       69.37        76.64        16.11        67.59        39.25        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ 
      121.25        29.82         9.50        72.39        31.23        27.02 
TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KQ 
      108.13       113.92        35.57        16.37        46.49        88.01 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       95.18       153.63       127.50        68.25        44.84         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
       58.55       152.15        31.79        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
       23.64        39.35        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 
       90.08        53.03        61.08        77.00        79.07        61.05 
TCGA-OR-A5LR TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5H9 
       28.04        18.05        38.50        24.85        20.25 

  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                         0.00                          4.11 
  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                        83.80                        153.63 
  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                        21.76                         44.55 
[1] "0.0 - 83.8 (21.8)"  "4.1 - 153.6 (44.5)"
[1] "hr=" "2.9"
D23V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  5(4Q34.3) MUTATED         1       11         3        9
  DEL PEAK  5(4Q34.3) WILD-TYPE       8       32        15        9
D23V3, multiclass
           clus
vv          DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE
  STAGE I                             1                             8
  STAGE II                           11                            32
  STAGE III                           3                            15
  STAGE IV                            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"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  5(4Q34.3) MUTATED    1 11  2 10
  DEL PEAK  5(4Q34.3) WILD-TYPE  8 37  9 10
D23V4, multiclass
    clus
vv   DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE
  T1                           1                             8
  T2                          11                            37
  T3                           2                             9
  T4                          10                            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"
D23V5, binary
                               cls
clus                             0  1
  DEL PEAK  5(4Q34.3) MUTATED   21  3
  DEL PEAK  5(4Q34.3) WILD-TYPE 57  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4Q34.3) MUTATED     21    3
  DEL PEAK  5(4Q34.3) WILD-TYPE   57    7
   clus
vv  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE
  0                          21                            57
  1                           3                             7
[1] 2 2
[1] FALSE
D23V6, binary
                               cls
clus                             0  1
  DEL PEAK  5(4Q34.3) MUTATED   16  9
  DEL PEAK  5(4Q34.3) WILD-TYPE 43 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4Q34.3) MUTATED     16    9
  DEL PEAK  5(4Q34.3) WILD-TYPE   43   22
        clus
vv       DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE
  FEMALE                          16                            43
  MALE                             9                            22
[1] 2 2
[1] FALSE
D23V7, binary
                               cls
clus                             0  1
  DEL PEAK  5(4Q34.3) MUTATED   18  6
  DEL PEAK  5(4Q34.3) WILD-TYPE 51 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4Q34.3) MUTATED     18    6
  DEL PEAK  5(4Q34.3) WILD-TYPE   51   12
     clus
vv    DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE
  NO                           18                            51
  YES                           6                            12
[1] 2 2
[1] FALSE
                               vv
clus                            ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK  5(4Q34.3) MUTATED                                       0
  DEL PEAK  5(4Q34.3) WILD-TYPE                                     1
                               vv
clus                            ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK  5(4Q34.3) MUTATED                                          0
  DEL PEAK  5(4Q34.3) WILD-TYPE                                        4
                               vv
clus                            ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK  5(4Q34.3) MUTATED                                     25
  DEL PEAK  5(4Q34.3) WILD-TYPE                                   60
D23V8, multiclass
                                          clus
vv                                         DEL PEAK  5(4Q34.3) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                              0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                           0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                              25
                                          clus
vv                                         DEL PEAK  5(4Q34.3) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                             4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  5(4Q34.3) MUTATED   13  4  7  0
  DEL PEAK  5(4Q34.3) WILD-TYPE 50  3  5  5
D23V9, multiclass
    clus
vv   DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE
  R0                          13                            50
  R1                           4                             3
  R2                           7                             5
  RX                           0                             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"
D23V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(4Q34.3) MUTATED       1                         0    21
  DEL PEAK  5(4Q34.3) WILD-TYPE     1                         1    55
D23V11, multiclass
                           clus
vv                          DEL PEAK  5(4Q34.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              21
                           clus
vv                          DEL PEAK  5(4Q34.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, binary
                               cls
clus                             0  1
  DEL PEAK  5(4Q34.3) MUTATED    2 11
  DEL PEAK  5(4Q34.3) WILD-TYPE  6 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4Q34.3) MUTATED      2   11
  DEL PEAK  5(4Q34.3) WILD-TYPE    6   27
                        clus
vv                       DEL PEAK  5(4Q34.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          11
                        clus
vv                       DEL PEAK  5(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            27
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK  6(4Q34.3) MUTATION ANALYSIS
D24V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(4Q34.3) MUTATED   14 14
  DEL PEAK  6(4Q34.3) WILD-TYPE 43 19
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           28                            62 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           14                            19 
$`DEL PEAK  6(4Q34.3) MUTATED`
TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA 
       39.58        42.51        13.91        16.11        44.45        30.31 
TCGA-OR-A5JB TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JS 
       18.12        49.22        18.48        15.25        36.26        12.59 
TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KB 
       66.51        18.15        32.68        16.37        24.62        24.36 
TCGA-OR-A5KX TCGA-OR-A5L2 TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LI TCGA-OR-A5LN 
       44.84        60.89         5.23        21.76        14.33        77.00 
TCGA-OR-A5LO TCGA-OR-A5LS TCGA-PK-A5HA TCGA-PK-A5HC 
       79.07        36.03        39.48        22.32 

$`DEL PEAK  6(4Q34.3) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-OR-A5J1 TCGA-OR-A5J2 
       33.83        91.30        43.30        12.59        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JC TCGA-OR-A5JD 
       68.75        12.00        88.87        19.04        57.53        99.88 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW 
       67.59        39.25       121.25        29.82         9.50        72.39 
TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 
       31.23        27.02       108.13       113.92        35.57        49.08 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        46.49        88.01        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 
      127.50        68.25        12.85         4.11        58.55       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD 
       31.79        28.31        29.10        28.64        23.64        39.35 
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        90.08        53.03 
TCGA-OR-A5LM TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       61.08        61.05        28.04        18.05        38.50         0.00 
TCGA-PA-A5YG TCGA-PK-A5H9 
       24.85        20.25 

  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                         5.23                          0.00 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                        79.07                        153.63 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                       27.465                        45.520 
[1] "5.2 - 79.1 (27.5)"  "0.0 - 153.6 (45.5)"
[1] "hr=" "2.4"
D24V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  6(4Q34.3) MUTATED         1       12         5        9
  DEL PEAK  6(4Q34.3) WILD-TYPE       8       31        13        9
D24V3, multiclass
           clus
vv          DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  STAGE I                             1                             8
  STAGE II                           12                            31
  STAGE III                           5                            13
  STAGE IV                            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"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  6(4Q34.3) MUTATED    1 13  3 10
  DEL PEAK  6(4Q34.3) WILD-TYPE  8 35  8 10
D24V4, multiclass
    clus
vv   DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  T1                           1                             8
  T2                          13                            35
  T3                           3                             8
  T4                          10                            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"
D24V5, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q34.3) MUTATED   24  3
  DEL PEAK  6(4Q34.3) WILD-TYPE 54  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED     24    3
  DEL PEAK  6(4Q34.3) WILD-TYPE   54    7
   clus
vv  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  0                          24                            54
  1                           3                             7
[1] 2 2
[1] FALSE
D24V6, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q34.3) MUTATED   19  9
  DEL PEAK  6(4Q34.3) WILD-TYPE 40 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED     19    9
  DEL PEAK  6(4Q34.3) WILD-TYPE   40   22
        clus
vv       DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  FEMALE                          19                            40
  MALE                             9                            22
[1] 2 2
[1] FALSE
D24V7, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q34.3) MUTATED   19  8
  DEL PEAK  6(4Q34.3) WILD-TYPE 50 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED     19    8
  DEL PEAK  6(4Q34.3) WILD-TYPE   50   10
     clus
vv    DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  NO                           19                            50
  YES                           8                            10
[1] 2 2
[1] FALSE
                               vv
clus                            ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK  6(4Q34.3) MUTATED                                       1
  DEL PEAK  6(4Q34.3) WILD-TYPE                                     0
                               vv
clus                            ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK  6(4Q34.3) MUTATED                                          0
  DEL PEAK  6(4Q34.3) WILD-TYPE                                        4
                               vv
clus                            ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK  6(4Q34.3) MUTATED                                     27
  DEL PEAK  6(4Q34.3) WILD-TYPE                                   58
D24V8, multiclass
                                          clus
vv                                         DEL PEAK  6(4Q34.3) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                           0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                              27
                                          clus
vv                                         DEL PEAK  6(4Q34.3) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                             4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  6(4Q34.3) MUTATED   17  5  5  0
  DEL PEAK  6(4Q34.3) WILD-TYPE 46  2  7  5
D24V9, multiclass
    clus
vv   DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  R0                          17                            46
  R1                           5                             2
  R2                           5                             7
  RX                           0                             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"
D24V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(4Q34.3) MUTATED       1                         0    22
  DEL PEAK  6(4Q34.3) WILD-TYPE     1                         1    54
D24V11, multiclass
                           clus
vv                          DEL PEAK  6(4Q34.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              22
                           clus
vv                          DEL PEAK  6(4Q34.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V12, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q34.3) MUTATED    3  9
  DEL PEAK  6(4Q34.3) WILD-TYPE  5 29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED      3    9
  DEL PEAK  6(4Q34.3) WILD-TYPE    5   29
                        clus
vv                       DEL PEAK  6(4Q34.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                           9
                        clus
vv                       DEL PEAK  6(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            29
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK  7(4Q35.1) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  7(4Q35.1) MUTATED   15 15
  DEL PEAK  7(4Q35.1) WILD-TYPE 42 18
  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                           30                            60 
  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                           15                            18 
$`DEL PEAK  7(4Q35.1) MUTATED`
TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JB 
       39.58        42.51        13.91        16.11        44.45        18.12 
TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JS 
       57.53        69.21        49.22        18.48        15.25        12.59 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K8 
       66.51        31.23        18.15        32.68        16.37        24.62 
TCGA-OR-A5KB TCGA-OR-A5KW TCGA-OR-A5L2 TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LI 
       24.36        68.25        60.89         5.23        21.76        14.33 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LS TCGA-P6-A5OH TCGA-PK-A5HA TCGA-PK-A5HC 
       61.08        77.00        36.03         0.00        39.48        22.32 

$`DEL PEAK  7(4Q35.1) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-P6-A5OG TCGA-OR-A5J1 TCGA-OR-A5J2 
       33.83        91.30        43.30        12.59        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JD 
       68.75        12.00        88.87        19.04        30.31        99.88 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL 
       66.25        17.79        69.37        76.64        16.11        67.59 
TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW 
       39.25        36.26       121.25        29.82         9.50        72.39 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K9 
       27.02       108.13       113.92        35.57        49.08        11.31 
TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       46.49        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84        12.85         4.11        58.55       152.15        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF 
       28.31        29.10        28.64        23.64        39.35        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO 
       52.24        78.41        36.33        90.08        53.03        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5H9 
       61.05        28.04        18.05        38.50        24.85        20.25 

  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                         0.00                          4.11 
  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                        77.00                        153.63 
  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE 
                       27.925                        43.925 
[1] "0.0 - 77.0 (27.9)"  "4.1 - 153.6 (43.9)"
[1] "hr=" "2.4"
D25V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  7(4Q35.1) MUTATED         2       11         6        9
  DEL PEAK  7(4Q35.1) WILD-TYPE       7       32        12        9
D25V3, multiclass
           clus
vv          DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE
  STAGE I                             2                             7
  STAGE II                           11                            32
  STAGE III                           6                            12
  STAGE IV                            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"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  7(4Q35.1) MUTATED    2 12  4 10
  DEL PEAK  7(4Q35.1) WILD-TYPE  7 36  7 10
D25V4, multiclass
    clus
vv   DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE
  T1                           2                             7
  T2                          12                            36
  T3                           4                             7
  T4                          10                            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  7(4Q35.1) MUTATED   25  3
  DEL PEAK  7(4Q35.1) WILD-TYPE 53  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q35.1) MUTATED     25    3
  DEL PEAK  7(4Q35.1) WILD-TYPE   53    7
   clus
vv  DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE
  0                          25                            53
  1                           3                             7
[1] 2 2
[1] FALSE
D25V6, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q35.1) MUTATED   18 12
  DEL PEAK  7(4Q35.1) WILD-TYPE 41 19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q35.1) MUTATED     18   12
  DEL PEAK  7(4Q35.1) WILD-TYPE   41   19
        clus
vv       DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE
  FEMALE                          18                            41
  MALE                            12                            19
[1] 2 2
[1] FALSE
D25V7, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q35.1) MUTATED   18 10
  DEL PEAK  7(4Q35.1) WILD-TYPE 51  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q35.1) MUTATED     18   10
  DEL PEAK  7(4Q35.1) WILD-TYPE   51    8
     clus
vv    DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE
  NO                           18                            51
  YES                          10                             8
[1] 2 2
[1] FALSE
                               vv
clus                            ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK  7(4Q35.1) MUTATED                                       0
  DEL PEAK  7(4Q35.1) WILD-TYPE                                     1
                               vv
clus                            ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK  7(4Q35.1) MUTATED                                          0
  DEL PEAK  7(4Q35.1) WILD-TYPE                                        4
                               vv
clus                            ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK  7(4Q35.1) MUTATED                                     30
  DEL PEAK  7(4Q35.1) WILD-TYPE                                   55
D25V8, multiclass
                                          clus
vv                                         DEL PEAK  7(4Q35.1) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                              0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                           0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                              30
                                          clus
vv                                         DEL PEAK  7(4Q35.1) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                             4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  7(4Q35.1) MUTATED   18  4  6  0
  DEL PEAK  7(4Q35.1) WILD-TYPE 45  3  6  5
D25V9, multiclass
    clus
vv   DEL PEAK  7(4Q35.1) MUTATED DEL PEAK  7(4Q35.1) WILD-TYPE
  R0                          18                            45
  R1                           4                             3
  R2                           6                             6
  RX                           0                             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"
D25V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(4Q35.1) MUTATED       1                         0    24
  DEL PEAK  7(4Q35.1) WILD-TYPE     1                         1    52
D25V11, multiclass
                           clus
vv                          DEL PEAK  7(4Q35.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              24
                           clus
vv                          DEL PEAK  7(4Q35.1) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V12, binary
                               cls
clus                             0  1
  DEL PEAK  7(4Q35.1) MUTATED    3 10
  DEL PEAK  7(4Q35.1) WILD-TYPE  5 28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q35.1) MUTATED      3   10
  DEL PEAK  7(4Q35.1) WILD-TYPE    5   28
                        clus
vv                       DEL PEAK  7(4Q35.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          10
                        clus
vv                       DEL PEAK  7(4Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            28
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK  8(6P24.3) MUTATION ANALYSIS
D26V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(6P24.3) MUTATED   11  9
  DEL PEAK  8(6P24.3) WILD-TYPE 46 24
  DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE 
                           20                            70 
  DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE 
                            9                            24 
$`DEL PEAK  8(6P24.3) MUTATED`
TCGA-OR-A5K0 TCGA-P6-A5OG TCGA-OR-A5J8 TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH 
       33.83        12.59        19.04        99.88        17.79        69.37 
TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5KT TCGA-OR-A5L2 
       49.22        15.25        36.26        66.51        95.18        60.89 
TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LS TCGA-OR-A5LT 
        5.23        21.76        14.33        53.03        36.03        18.05 
TCGA-OU-A5PI TCGA-P6-A5OH 
       38.50         0.00 

$`DEL PEAK  8(6P24.3) WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J9 
       68.75        13.91        12.00        88.87        16.11        44.45 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JI 
       30.31        18.12        57.53        69.21        66.25        76.64 
TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5JS 
       16.11        67.59        18.48        39.25       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ 
       29.82         9.50        72.39        31.23        18.15        27.02 
TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
      108.13        32.68       113.92        35.57        16.37        49.08 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS 
       24.62        11.31        24.36        46.49        88.01        83.80 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       127.50        68.25        44.84        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
       58.55       152.15        31.79        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
       23.64        39.35        14.63        52.24        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       90.08        61.08        77.00        79.07        61.05        28.04 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       24.85        20.25        39.48        22.32 

  DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE 
                         0.00                          4.11 
  DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE 
                        99.88                        153.63 
  DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE 
                        34.93                         39.53 
[1] "0.0 - 99.9 (34.9)"  "4.1 - 153.6 (39.5)"
[1] "hr=" "1.6"
D26V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  8(6P24.3) MUTATED         1       10         2        7
  DEL PEAK  8(6P24.3) WILD-TYPE       8       33        16       11
D26V3, multiclass
           clus
vv          DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE
  STAGE I                             1                             8
  STAGE II                           10                            33
  STAGE III                           2                            16
  STAGE IV                            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"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  8(6P24.3) MUTATED    1 11  2  6
  DEL PEAK  8(6P24.3) WILD-TYPE  8 37  9 14
D26V4, multiclass
    clus
vv   DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE
  T1                           1                             8
  T2                          11                            37
  T3                           2                             9
  T4                           6                            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"
D26V5, binary
                               cls
clus                             0  1
  DEL PEAK  8(6P24.3) MUTATED   18  2
  DEL PEAK  8(6P24.3) WILD-TYPE 60  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(6P24.3) MUTATED     18    2
  DEL PEAK  8(6P24.3) WILD-TYPE   60    8
   clus
vv  DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE
  0                          18                            60
  1                           2                             8
[1] 2 2
[1] FALSE
D26V6, binary
                               cls
clus                             0  1
  DEL PEAK  8(6P24.3) MUTATED   13  7
  DEL PEAK  8(6P24.3) WILD-TYPE 46 24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(6P24.3) MUTATED     13    7
  DEL PEAK  8(6P24.3) WILD-TYPE   46   24
        clus
vv       DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE
  FEMALE                          13                            46
  MALE                             7                            24
[1] 2 2
[1] FALSE
D26V7, binary
                               cls
clus                             0  1
  DEL PEAK  8(6P24.3) MUTATED   17  2
  DEL PEAK  8(6P24.3) WILD-TYPE 52 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(6P24.3) MUTATED     17    2
  DEL PEAK  8(6P24.3) WILD-TYPE   52   16
     clus
vv    DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE
  NO                           17                            52
  YES                           2                            16
[1] 2 2
[1] FALSE
                               vv
clus                            ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK  8(6P24.3) MUTATED                                       1
  DEL PEAK  8(6P24.3) WILD-TYPE                                     0
                               vv
clus                            ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK  8(6P24.3) MUTATED                                          2
  DEL PEAK  8(6P24.3) WILD-TYPE                                        2
                               vv
clus                            ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK  8(6P24.3) MUTATED                                     17
  DEL PEAK  8(6P24.3) WILD-TYPE                                   68
D26V8, multiclass
                                          clus
vv                                         DEL PEAK  8(6P24.3) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                           2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                              17
                                          clus
vv                                         DEL PEAK  8(6P24.3) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                             2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  8(6P24.3) MUTATED   13  1  5  0
  DEL PEAK  8(6P24.3) WILD-TYPE 50  6  7  5
D26V9, multiclass
    clus
vv   DEL PEAK  8(6P24.3) MUTATED DEL PEAK  8(6P24.3) WILD-TYPE
  R0                          13                            50
  R1                           1                             6
  R2                           5                             7
  RX                           0                             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"
D26V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(6P24.3) MUTATED       0                         0    17
  DEL PEAK  8(6P24.3) WILD-TYPE     2                         1    59
D26V11, multiclass
                           clus
vv                          DEL PEAK  8(6P24.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              17
                           clus
vv                          DEL PEAK  8(6P24.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V12, binary
                               cls
clus                             0  1
  DEL PEAK  8(6P24.3) MUTATED    1  8
  DEL PEAK  8(6P24.3) WILD-TYPE  7 30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(6P24.3) MUTATED      1    8
  DEL PEAK  8(6P24.3) WILD-TYPE    7   30
                        clus
vv                       DEL PEAK  8(6P24.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           8
                        clus
vv                       DEL PEAK  8(6P24.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            30
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK  9(6Q26) MUTATION ANALYSIS
D27V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  9(6Q26) MUTATED   11 10
  DEL PEAK  9(6Q26) WILD-TYPE 46 23
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                         21                          69 
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                         10                          23 
$`DEL PEAK  9(6Q26) MUTATED`
TCGA-OR-A5K0 TCGA-P6-A5OG TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JG 
       33.83        12.59        16.11        18.12        99.88        17.79 
TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY 
       69.37        49.22        36.26        12.59        66.51        18.15 
TCGA-OR-A5K2 TCGA-OR-A5KO TCGA-OR-A5L2 TCGA-OR-A5LC TCGA-OR-A5LG TCGA-OR-A5LL 
       32.68        46.49        60.89         5.23        52.24        53.03 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OH 
       36.03        38.50         0.00 

$`DEL PEAK  9(6Q26) WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       91.30        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 
       68.75        13.91        12.00        88.87        19.04        44.45 
TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JJ 
       30.31        57.53        69.21        66.25        76.64        16.11 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT 
       67.59        18.48        39.25        15.25       121.25        29.82 
TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 
        9.50        72.39        31.23        27.02       108.13       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       35.57        16.37        49.08        24.62        11.31        24.36 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       88.01        83.80        95.18       153.63       127.50        68.25 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84        12.85         4.11        58.55       152.15        31.79 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LE 
       28.31        29.10        28.64        23.64        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM 
       14.63        78.41        14.33        36.33        90.08        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-PA-A5YG 
       77.00        79.07        61.05        28.04        18.05        24.85 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       20.25        39.48        22.32 

  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                       0.00                        4.11 
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                      99.88                      153.63 
  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE 
                      36.03                       39.48 
[1] "0.0 - 99.9 (36.0)"  "4.1 - 153.6 (39.5)"
[1] "hr=" "1.9"
D27V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  9(6Q26) MUTATED         0        9         3        9
  DEL PEAK  9(6Q26) WILD-TYPE       9       34        15        9
D27V3, multiclass
           clus
vv          DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  STAGE I                           0                           9
  STAGE II                          9                          34
  STAGE III                         3                          15
  STAGE IV                          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"
                             vv
clus                          T1 T2 T3 T4
  DEL PEAK  9(6Q26) MUTATED    0 10  2  9
  DEL PEAK  9(6Q26) WILD-TYPE  9 38  9 11
D27V4, multiclass
    clus
vv   DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  T1                         0                           9
  T2                        10                          38
  T3                         2                           9
  T4                         9                          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"
D27V5, binary
                             cls
clus                           0  1
  DEL PEAK  9(6Q26) MUTATED   18  3
  DEL PEAK  9(6Q26) WILD-TYPE 60  7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(6Q26) MUTATED     18    3
  DEL PEAK  9(6Q26) WILD-TYPE   60    7
   clus
vv  DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  0                        18                          60
  1                         3                           7
[1] 2 2
[1] FALSE
D27V6, binary
                             cls
clus                           0  1
  DEL PEAK  9(6Q26) MUTATED   16  5
  DEL PEAK  9(6Q26) WILD-TYPE 43 26
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(6Q26) MUTATED     16    5
  DEL PEAK  9(6Q26) WILD-TYPE   43   26
        clus
vv       DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  FEMALE                        16                          43
  MALE                           5                          26
[1] 2 2
[1] FALSE
D27V7, binary
                             cls
clus                           0  1
  DEL PEAK  9(6Q26) MUTATED   15  4
  DEL PEAK  9(6Q26) WILD-TYPE 54 14
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(6Q26) MUTATED     15    4
  DEL PEAK  9(6Q26) WILD-TYPE   54   14
     clus
vv    DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  NO                         15                          54
  YES                         4                          14
[1] 2 2
[1] FALSE
                             vv
clus                          ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK  9(6Q26) MUTATED                                       1
  DEL PEAK  9(6Q26) WILD-TYPE                                     0
                             vv
clus                          ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK  9(6Q26) MUTATED                                          2
  DEL PEAK  9(6Q26) WILD-TYPE                                        2
                             vv
clus                          ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK  9(6Q26) MUTATED                                     18
  DEL PEAK  9(6Q26) WILD-TYPE                                   67
D27V8, multiclass
                                          clus
vv                                         DEL PEAK  9(6Q26) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                            1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                         2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                            18
                                          clus
vv                                         DEL PEAK  9(6Q26) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                              0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                           2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                              67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          R0 R1 R2 RX
  DEL PEAK  9(6Q26) MUTATED   11  3  5  1
  DEL PEAK  9(6Q26) WILD-TYPE 52  4  7  4
D27V9, multiclass
    clus
vv   DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  R0                        11                          52
  R1                         3                           4
  R2                         5                           7
  RX                         1                           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"
D27V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(6Q26) MUTATED       0                         0    19
  DEL PEAK  9(6Q26) WILD-TYPE     2                         1    57
D27V11, multiclass
                           clus
vv                          DEL PEAK  9(6Q26) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            19
                           clus
vv                          DEL PEAK  9(6Q26) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V12, binary
                             cls
clus                           0  1
  DEL PEAK  9(6Q26) MUTATED    1  7
  DEL PEAK  9(6Q26) WILD-TYPE  7 31
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(6Q26) MUTATED      1    7
  DEL PEAK  9(6Q26) WILD-TYPE    7   31
                        clus
vv                       DEL PEAK  9(6Q26) MUTATED DEL PEAK  9(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             1                           7
  NOT HISPANIC OR LATINO                         7                          31
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK 10(7Q36.3) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 10(7Q36.3) MUTATED    3  8
  DEL PEAK 10(7Q36.3) WILD-TYPE 54 25
  DEL PEAK 10(7Q36.3) MUTATED DEL PEAK 10(7Q36.3) WILD-TYPE 
                           11                            79 
  DEL PEAK 10(7Q36.3) MUTATED DEL PEAK 10(7Q36.3) WILD-TYPE 
                            8                            25 
$`DEL PEAK 10(7Q36.3) MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JM TCGA-OR-A5K6 
       13.91        18.12        57.53        69.21        18.48        49.08 
TCGA-OR-A5L2 TCGA-OR-A5LD TCGA-OR-A5LI TCGA-OR-A5LT TCGA-PK-A5HC 
       60.89        39.35        14.33        18.05        22.32 

$`DEL PEAK 10(7Q36.3) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        68.75        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JG 
       19.04        44.45        30.31        99.88        66.25        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JO 
       69.37        76.64        16.11        49.22        67.59        39.25 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU 
       15.25        36.26       121.25        12.59        29.82         9.50 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 
       66.51        72.39        31.23        18.15        27.02       108.13 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 
       32.68       113.92        35.57        16.37        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       24.36        46.49        88.01        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      127.50        68.25        44.84        12.85         4.11        58.55 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        28.31        29.10        28.64        23.64 
TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
        5.23        21.76        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 
       90.08        53.03        61.08        77.00        79.07        61.05 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 
       28.04        36.03        38.50         0.00        24.85        20.25 
TCGA-PK-A5HA 
       39.48 

  DEL PEAK 10(7Q36.3) MUTATED DEL PEAK 10(7Q36.3) WILD-TYPE 
                        13.91                          0.00 
  DEL PEAK 10(7Q36.3) MUTATED DEL PEAK 10(7Q36.3) WILD-TYPE 
                        69.21                        153.63 
  DEL PEAK 10(7Q36.3) MUTATED DEL PEAK 10(7Q36.3) WILD-TYPE 
                        22.32                         39.25 
[1] "13.9 - 69.2 (22.3)" "0.0 - 153.6 (39.2)"
[1] "hr=" "2.9"
D28V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 10(7Q36.3) MUTATED         1        2         3        4
  DEL PEAK 10(7Q36.3) WILD-TYPE       8       41        15       14
D28V3, multiclass
           clus
vv          DEL PEAK 10(7Q36.3) MUTATED DEL PEAK 10(7Q36.3) WILD-TYPE
  STAGE I                             1                             8
  STAGE II                            2                            41
  STAGE III                           3                            15
  STAGE IV                            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"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 10(7Q36.3) MUTATED    1  2  2  5
  DEL PEAK 10(7Q36.3) WILD-TYPE  8 46  9 15
D28V4, multiclass
    clus
vv   DEL PEAK 10(7Q36.3) MUTATED DEL PEAK 10(7Q36.3) WILD-TYPE
  T1                           1                             8
  T2                           2                            46
  T3                           2                             9
  T4                           5                            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"
D28V5, binary
                               cls
clus                             0  1
  DEL PEAK 10(7Q36.3) MUTATED    9  1
  DEL PEAK 10(7Q36.3) WILD-TYPE 69  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(7Q36.3) MUTATED      9    1
  DEL PEAK 10(7Q36.3) WILD-TYPE   69    9
   clus
vv  DEL PEAK 10(7Q36.3) MUTATED DEL PEAK 10(7Q36.3) WILD-TYPE
  0                           9                            69
  1                           1                             9
[1] 2 2
[1] FALSE
D28V6, binary
                               cls
clus                             0  1
  DEL PEAK 10(7Q36.3) MUTATED    7  4
  DEL PEAK 10(7Q36.3) WILD-TYPE 52 27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(7Q36.3) MUTATED      7    4
  DEL PEAK 10(7Q36.3) WILD-TYPE   52   27
        clus
vv       DEL PEAK 10(7Q36.3) MUTATED DEL PEAK 10(7Q36.3) WILD-TYPE
  FEMALE                           7                            52
  MALE                             4                            27
[1] 2 2
[1] FALSE
D28V7, binary
                               cls
clus                             0  1
  DEL PEAK 10(7Q36.3) MUTATED    8  1
  DEL PEAK 10(7Q36.3) WILD-TYPE 61 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(7Q36.3) MUTATED      8    1
  DEL PEAK 10(7Q36.3) WILD-TYPE   61   17
     clus
vv    DEL PEAK 10(7Q36.3) MUTATED DEL PEAK 10(7Q36.3) WILD-TYPE
  NO                            8                            61
  YES                           1                            17
[1] 2 2
[1] FALSE
                               vv
clus                            ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK 10(7Q36.3) MUTATED                                       0
  DEL PEAK 10(7Q36.3) WILD-TYPE                                     1
                               vv
clus                            ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK 10(7Q36.3) MUTATED                                          0
  DEL PEAK 10(7Q36.3) WILD-TYPE                                        4
                               vv
clus                            ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK 10(7Q36.3) MUTATED                                     11
  DEL PEAK 10(7Q36.3) WILD-TYPE                                   74
D28V8, multiclass
                                          clus
vv                                         DEL PEAK 10(7Q36.3) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                              0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                           0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                              11
                                          clus
vv                                         DEL PEAK 10(7Q36.3) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                             4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 10(7Q36.3) MUTATED    4  3  2  1
  DEL PEAK 10(7Q36.3) WILD-TYPE 59  4 10  4
D28V9, multiclass
    clus
vv   DEL PEAK 10(7Q36.3) MUTATED DEL PEAK 10(7Q36.3) WILD-TYPE
  R0                           4                            59
  R1                           3                             4
  R2                           2                            10
  RX                           1                             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"
D28V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(7Q36.3) MUTATED       1                         0     9
  DEL PEAK 10(7Q36.3) WILD-TYPE     1                         1    67
D28V11, multiclass
                           clus
vv                          DEL PEAK 10(7Q36.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               9
                           clus
vv                          DEL PEAK 10(7Q36.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V12, binary
                               cls
clus                             0  1
  DEL PEAK 10(7Q36.3) MUTATED    1  5
  DEL PEAK 10(7Q36.3) WILD-TYPE  7 33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(7Q36.3) MUTATED      1    5
  DEL PEAK 10(7Q36.3) WILD-TYPE    7   33
                        clus
vv                       DEL PEAK 10(7Q36.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           5
                        clus
vv                       DEL PEAK 10(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            33
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK 11(9P23) MUTATION ANALYSIS
D29V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 11(9P23) MUTATED   11 12
  DEL PEAK 11(9P23) WILD-TYPE 46 21
  DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE 
                         23                          67 
  DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE 
                         12                          21 
$`DEL PEAK 11(9P23) MUTATED`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-P6-A5OG TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 
       33.83        91.30        12.59        16.11        19.04        44.45 
TCGA-OR-A5JC TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JV 
       57.53        49.22        18.48        15.25        12.59        66.51 
TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5KB TCGA-OR-A5KZ TCGA-OR-A5L2 
       18.15        32.68        16.37        24.36         4.11        60.89 
TCGA-OR-A5L3 TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LM 
      152.15         5.23        21.76        52.24        61.08 

$`DEL PEAK 11(9P23) WILD-TYPE`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       43.30        39.58        42.51        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD 
       13.91        12.00        88.87        30.31        18.12        99.88 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU 
       67.59        39.25        36.26       121.25        29.82         9.50 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 
       72.39        31.23        27.02       108.13       113.92        35.57 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS 
       49.08        24.62        11.31        46.49        88.01        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       95.18       153.63       127.50        68.25        44.84        12.85 
TCGA-OR-A5L1 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       58.55        31.79        28.31        29.10        28.64        23.64 
TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK 
       39.35        14.63        78.41        14.33        36.33        90.08 
TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       53.03        77.00        79.07        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       18.05        38.50         0.00        24.85        20.25        39.48 
TCGA-PK-A5HC 
       22.32 

  DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE 
                       4.11                        0.00 
  DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE 
                     152.15                      153.63 
  DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE 
                      24.36                       39.48 
[1] "4.1 - 152.2 (24.4)" "0.0 - 153.6 (39.5)"
[1] "hr=" "2.1"
D29V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 11(9P23) MUTATED         1       11         5        5
  DEL PEAK 11(9P23) WILD-TYPE       8       32        13       13
D29V3, multiclass
           clus
vv          DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE
  STAGE I                           1                           8
  STAGE II                         11                          32
  STAGE III                         5                          13
  STAGE IV                          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"
                             vv
clus                          T1 T2 T3 T4
  DEL PEAK 11(9P23) MUTATED    1 11  4  6
  DEL PEAK 11(9P23) WILD-TYPE  8 37  7 14
D29V4, multiclass
    clus
vv   DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE
  T1                         1                           8
  T2                        11                          37
  T3                         4                           7
  T4                         6                          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"
D29V5, binary
                             cls
clus                           0  1
  DEL PEAK 11(9P23) MUTATED   21  1
  DEL PEAK 11(9P23) WILD-TYPE 57  9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(9P23) MUTATED     21    1
  DEL PEAK 11(9P23) WILD-TYPE   57    9
   clus
vv  DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE
  0                        21                          57
  1                         1                           9
[1] 2 2
[1] FALSE
D29V6, binary
                             cls
clus                           0  1
  DEL PEAK 11(9P23) MUTATED   14  9
  DEL PEAK 11(9P23) WILD-TYPE 45 22
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(9P23) MUTATED     14    9
  DEL PEAK 11(9P23) WILD-TYPE   45   22
        clus
vv       DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE
  FEMALE                        14                          45
  MALE                           9                          22
[1] 2 2
[1] FALSE
D29V7, binary
                             cls
clus                           0  1
  DEL PEAK 11(9P23) MUTATED   15  7
  DEL PEAK 11(9P23) WILD-TYPE 54 11
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(9P23) MUTATED     15    7
  DEL PEAK 11(9P23) WILD-TYPE   54   11
     clus
vv    DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE
  NO                         15                          54
  YES                         7                          11
[1] 2 2
[1] FALSE
                             vv
clus                          ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK 11(9P23) MUTATED                                       0
  DEL PEAK 11(9P23) WILD-TYPE                                     1
                             vv
clus                          ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK 11(9P23) MUTATED                                          0
  DEL PEAK 11(9P23) WILD-TYPE                                        4
                             vv
clus                          ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK 11(9P23) MUTATED                                     23
  DEL PEAK 11(9P23) WILD-TYPE                                   62
D29V8, multiclass
                                          clus
vv                                         DEL PEAK 11(9P23) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                            0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                         0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                            23
                                          clus
vv                                         DEL PEAK 11(9P23) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                              1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                           4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                              62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          R0 R1 R2 RX
  DEL PEAK 11(9P23) MUTATED   14  2  4  2
  DEL PEAK 11(9P23) WILD-TYPE 49  5  8  3
D29V9, multiclass
    clus
vv   DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE
  R0                        14                          49
  R1                         2                           5
  R2                         4                           8
  RX                         2                           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"
D29V10, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(9P23) MUTATED       0                         0    22
  DEL PEAK 11(9P23) WILD-TYPE     2                         1    54
D29V11, multiclass
                           clus
vv                          DEL PEAK 11(9P23) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            22
                           clus
vv                          DEL PEAK 11(9P23) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V12, binary
                             cls
clus                           0  1
  DEL PEAK 11(9P23) MUTATED    3  9
  DEL PEAK 11(9P23) WILD-TYPE  5 29
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(9P23) MUTATED      3    9
  DEL PEAK 11(9P23) WILD-TYPE    5   29
                        clus
vv                       DEL PEAK 11(9P23) MUTATED DEL PEAK 11(9P23) WILD-TYPE
  HISPANIC OR LATINO                             3                           5
  NOT HISPANIC OR LATINO                         9                          29
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK 12(9P21.3) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 12(9P21.3) MUTATED   13 13
  DEL PEAK 12(9P21.3) WILD-TYPE 44 20
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           26                            64 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           13                            20 
$`DEL PEAK 12(9P21.3) MUTATED`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-P6-A5OG TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 
       33.83        91.30        12.59        16.11        19.04        44.45 
TCGA-OR-A5JC TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JT 
       57.53        49.22        18.48        15.25        12.59        29.82 
TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
       66.51        18.15        32.68        16.37        49.08        11.31 
TCGA-OR-A5KB TCGA-OR-A5KZ TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5LC TCGA-OR-A5LE 
       24.36         4.11        60.89       152.15         5.23        21.76 
TCGA-OR-A5LG TCGA-OR-A5LM 
       52.24        61.08 

$`DEL PEAK 12(9P21.3) WILD-TYPE`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       43.30        39.58        42.51        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD 
       13.91        12.00        88.87        30.31        18.12        99.88 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JU TCGA-OR-A5JW 
       67.59        39.25        36.26       121.25         9.50        72.39 
TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K8 
       31.23        27.02       108.13       113.92        35.57        24.62 
TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       46.49        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L1 TCGA-OR-A5L4 TCGA-OR-A5L6 
       68.25        44.84        12.85        58.55        31.79        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH 
       29.10        28.64        23.64        39.35        14.63        78.41 
TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO 
       14.33        36.33        90.08        53.03        77.00        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       61.05        28.04        36.03        18.05        38.50         0.00 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       24.85        20.25        39.48        22.32 

  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                         4.11                          0.00 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                       152.15                        153.63 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                        27.09                         39.53 
[1] "4.1 - 152.2 (27.1)" "0.0 - 153.6 (39.5)"
[1] "hr=" "2.2"
D30V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 12(9P21.3) MUTATED         1       14         5        5
  DEL PEAK 12(9P21.3) WILD-TYPE       8       29        13       13
D30V3, multiclass
           clus
vv          DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  STAGE I                             1                             8
  STAGE II                           14                            29
  STAGE III                           5                            13
  STAGE IV                            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"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 12(9P21.3) MUTATED    1 14  4  6
  DEL PEAK 12(9P21.3) WILD-TYPE  8 34  7 14
D30V4, multiclass
    clus
vv   DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  T1                           1                             8
  T2                          14                            34
  T3                           4                             7
  T4                           6                            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"
D30V5, binary
                               cls
clus                             0  1
  DEL PEAK 12(9P21.3) MUTATED   24  1
  DEL PEAK 12(9P21.3) WILD-TYPE 54  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P21.3) MUTATED     24    1
  DEL PEAK 12(9P21.3) WILD-TYPE   54    9
   clus
vv  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  0                          24                            54
  1                           1                             9
[1] 2 2
[1] FALSE
D30V6, binary
                               cls
clus                             0  1
  DEL PEAK 12(9P21.3) MUTATED   17  9
  DEL PEAK 12(9P21.3) WILD-TYPE 42 22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P21.3) MUTATED     17    9
  DEL PEAK 12(9P21.3) WILD-TYPE   42   22
        clus
vv       DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  FEMALE                          17                            42
  MALE                             9                            22
[1] 2 2
[1] FALSE
D30V7, binary
                               cls
clus                             0  1
  DEL PEAK 12(9P21.3) MUTATED   17  8
  DEL PEAK 12(9P21.3) WILD-TYPE 52 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P21.3) MUTATED     17    8
  DEL PEAK 12(9P21.3) WILD-TYPE   52   10
     clus
vv    DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  NO                           17                            52
  YES                           8                            10
[1] 2 2
[1] FALSE
                               vv
clus                            ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK 12(9P21.3) MUTATED                                       0
  DEL PEAK 12(9P21.3) WILD-TYPE                                     1
                               vv
clus                            ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK 12(9P21.3) MUTATED                                          0
  DEL PEAK 12(9P21.3) WILD-TYPE                                        4
                               vv
clus                            ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK 12(9P21.3) MUTATED                                     26
  DEL PEAK 12(9P21.3) WILD-TYPE                                   59
D30V8, multiclass
                                          clus
vv                                         DEL PEAK 12(9P21.3) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                              0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                           0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                              26
                                          clus
vv                                         DEL PEAK 12(9P21.3) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                             4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 12(9P21.3) MUTATED   17  2  4  2
  DEL PEAK 12(9P21.3) WILD-TYPE 46  5  8  3
D30V9, multiclass
    clus
vv   DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  R0                          17                            46
  R1                           2                             5
  R2                           4                             8
  RX                           2                             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"
D30V10, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(9P21.3) MUTATED       0                         0    25
  DEL PEAK 12(9P21.3) WILD-TYPE     2                         1    51
D30V11, multiclass
                           clus
vv                          DEL PEAK 12(9P21.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              25
                           clus
vv                          DEL PEAK 12(9P21.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V12, binary
                               cls
clus                             0  1
  DEL PEAK 12(9P21.3) MUTATED    3 10
  DEL PEAK 12(9P21.3) WILD-TYPE  5 28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P21.3) MUTATED      3   10
  DEL PEAK 12(9P21.3) WILD-TYPE    5   28
                        clus
vv                       DEL PEAK 12(9P21.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          10
                        clus
vv                       DEL PEAK 12(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            28
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK 13(10Q23.1) MUTATION ANALYSIS
D31V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 13(10Q23.1) MUTATED    6  4
  DEL PEAK 13(10Q23.1) WILD-TYPE 51 29
  DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE 
                            10                             80 
  DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE 
                             4                             29 
$`DEL PEAK 13(10Q23.1) MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV 
       30.31        17.79        69.37        36.26        12.59        66.51 
TCGA-OR-A5JY TCGA-OR-A5L2 TCGA-OR-A5L6 TCGA-PK-A5HC 
       18.15        60.89        28.31        22.32 

$`DEL PEAK 13(10Q23.1) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB 
       33.83        91.30        43.30        39.58        12.59        42.51 
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        68.75        13.91        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        44.45        18.12        57.53        99.88 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       69.21        66.25        76.64        16.11        49.22        67.59 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU 
       18.48        39.25        15.25       121.25        29.82         9.50 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       72.39        31.23        27.02       108.13        32.68       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       35.57        16.37        49.08        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       46.49        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 
       68.25        44.84        12.85         4.11        58.55       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       31.79        29.10        28.64        23.64         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ 
       21.76        14.63        52.24        78.41        14.33        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP 
       90.08        53.03        61.08        77.00        79.07        61.05 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG 
       28.04        36.03        18.05        38.50         0.00        24.85 
TCGA-PK-A5H9 TCGA-PK-A5HA 
       20.25        39.48 

  DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE 
                         12.59                           0.00 
  DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE 
                         69.37                         153.63 
  DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE 
                        29.310                         39.415 
[1] "12.6 - 69.4 (29.3)" "0.0 - 153.6 (39.4)"
[1] "hr=" "1.3"
D31V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 13(10Q23.1) MUTATED         0        6         1        3
  DEL PEAK 13(10Q23.1) WILD-TYPE       9       37        17       15
D31V3, multiclass
           clus
vv          DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE
  STAGE I                              0                              9
  STAGE II                             6                             37
  STAGE III                            1                             17
  STAGE IV                             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"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 13(10Q23.1) MUTATED    0  6  0  4
  DEL PEAK 13(10Q23.1) WILD-TYPE  9 42 11 16
D31V4, multiclass
    clus
vv   DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE
  T1                            0                              9
  T2                            6                             42
  T3                            0                             11
  T4                            4                             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"
D31V5, binary
                                cls
clus                              0  1
  DEL PEAK 13(10Q23.1) MUTATED    8  2
  DEL PEAK 13(10Q23.1) WILD-TYPE 70  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q23.1) MUTATED      8    2
  DEL PEAK 13(10Q23.1) WILD-TYPE   70    8
   clus
vv  DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE
  0                            8                             70
  1                            2                              8
[1] 2 2
[1] FALSE
D31V6, binary
                                cls
clus                              0  1
  DEL PEAK 13(10Q23.1) MUTATED    7  3
  DEL PEAK 13(10Q23.1) WILD-TYPE 52 28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q23.1) MUTATED      7    3
  DEL PEAK 13(10Q23.1) WILD-TYPE   52   28
        clus
vv       DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE
  FEMALE                            7                             52
  MALE                              3                             28
[1] 2 2
[1] FALSE
D31V7, binary
                                cls
clus                              0  1
  DEL PEAK 13(10Q23.1) MUTATED    7  2
  DEL PEAK 13(10Q23.1) WILD-TYPE 62 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q23.1) MUTATED      7    2
  DEL PEAK 13(10Q23.1) WILD-TYPE   62   16
     clus
vv    DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE
  NO                             7                             62
  YES                            2                             16
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK 13(10Q23.1) MUTATED                                       1
  DEL PEAK 13(10Q23.1) WILD-TYPE                                     0
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK 13(10Q23.1) MUTATED                                          1
  DEL PEAK 13(10Q23.1) WILD-TYPE                                        3
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK 13(10Q23.1) MUTATED                                      8
  DEL PEAK 13(10Q23.1) WILD-TYPE                                   77
D31V8, multiclass
                                          clus
vv                                         DEL PEAK 13(10Q23.1) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                8
                                          clus
vv                                         DEL PEAK 13(10Q23.1) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 13(10Q23.1) MUTATED    6  3  1  0
  DEL PEAK 13(10Q23.1) WILD-TYPE 57  4 11  5
D31V9, multiclass
    clus
vv   DEL PEAK 13(10Q23.1) MUTATED DEL PEAK 13(10Q23.1) WILD-TYPE
  R0                            6                             57
  R1                            3                              4
  R2                            1                             11
  RX                            0                              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"
D31V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(10Q23.1) MUTATED       1                         0     9
  DEL PEAK 13(10Q23.1) WILD-TYPE     1                         1    67
D31V11, multiclass
                           clus
vv                          DEL PEAK 13(10Q23.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                9
                           clus
vv                          DEL PEAK 13(10Q23.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V12, binary
                                cls
clus                              0  1
  DEL PEAK 13(10Q23.1) MUTATED    0  3
  DEL PEAK 13(10Q23.1) WILD-TYPE  8 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q23.1) MUTATED      0    3
  DEL PEAK 13(10Q23.1) WILD-TYPE    8   35
                        clus
vv                       DEL PEAK 13(10Q23.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            3
                        clus
vv                       DEL PEAK 13(10Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                             35
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK 14(11P15.5) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 14(11P15.5) MUTATED   19  7
  DEL PEAK 14(11P15.5) WILD-TYPE 38 26
  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                            26                             64 
  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                             7                             26 
$`DEL PEAK 14(11P15.5) MUTATED`
TCGA-PK-A5HB TCGA-OR-A5J4 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG 
       42.51        13.91        30.31        57.53        99.88        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5JW 
       69.37        76.64        49.22        36.26        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KW 
       31.23        18.15        49.08        11.31        24.36        68.25 
TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OR-A5LT 
       28.31         5.23        61.08        77.00        36.03        18.05 
TCGA-OU-A5PI TCGA-PK-A5HA 
       38.50        39.48 

$`DEL PEAK 14(11P15.5) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J1 
       33.83        91.30        43.30        39.58        12.59        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       55.13        68.75        12.00        88.87        16.11        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL 
       44.45        18.12        69.21        66.25        16.11        67.59 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT 
       18.48        39.25        15.25       121.25        12.59        29.82 
TCGA-OR-A5JU TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
        9.50        27.02       108.13        32.68       113.92        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       16.37        24.62        46.49        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      153.63       127.50        44.84        12.85         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       60.89       152.15        31.79        29.10        28.64        23.64 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI 
       39.35        21.76        14.63        52.24        78.41        14.33 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        90.08        53.03        79.07        61.05        28.04 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
        0.00        24.85        20.25        22.32 

  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                          5.23                           0.00 
  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                         99.88                         153.63 
  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE 
                         38.99                          37.79 
[1] "5.2 - 99.9 (39.0)"  "0.0 - 153.6 (37.8)"
[1] "hr=" "1.4"
D32V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 14(11P15.5) MUTATED         2       12         3        7
  DEL PEAK 14(11P15.5) WILD-TYPE       7       31        15       11
D32V3, multiclass
           clus
vv          DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE
  STAGE I                              2                              7
  STAGE II                            12                             31
  STAGE III                            3                             15
  STAGE IV                             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"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 14(11P15.5) MUTATED    2 14  3  5
  DEL PEAK 14(11P15.5) WILD-TYPE  7 34  8 15
D32V4, multiclass
    clus
vv   DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE
  T1                            2                              7
  T2                           14                             34
  T3                            3                              8
  T4                            5                             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 14(11P15.5) MUTATED   19  5
  DEL PEAK 14(11P15.5) WILD-TYPE 59  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11P15.5) MUTATED     19    5
  DEL PEAK 14(11P15.5) WILD-TYPE   59    5
   clus
vv  DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE
  0                           19                             59
  1                            5                              5
[1] 2 2
[1] FALSE
D32V6, binary
                                cls
clus                              0  1
  DEL PEAK 14(11P15.5) MUTATED   14 12
  DEL PEAK 14(11P15.5) WILD-TYPE 45 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11P15.5) MUTATED     14   12
  DEL PEAK 14(11P15.5) WILD-TYPE   45   19
        clus
vv       DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE
  FEMALE                           14                             45
  MALE                             12                             19
[1] 2 2
[1] FALSE
D32V7, binary
                                cls
clus                              0  1
  DEL PEAK 14(11P15.5) MUTATED   18  6
  DEL PEAK 14(11P15.5) WILD-TYPE 51 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11P15.5) MUTATED     18    6
  DEL PEAK 14(11P15.5) WILD-TYPE   51   12
     clus
vv    DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE
  NO                            18                             51
  YES                            6                             12
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK 14(11P15.5) MUTATED                                       1
  DEL PEAK 14(11P15.5) WILD-TYPE                                     0
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK 14(11P15.5) MUTATED                                          2
  DEL PEAK 14(11P15.5) WILD-TYPE                                        2
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK 14(11P15.5) MUTATED                                     23
  DEL PEAK 14(11P15.5) WILD-TYPE                                   62
D32V8, multiclass
                                          clus
vv                                         DEL PEAK 14(11P15.5) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               23
                                          clus
vv                                         DEL PEAK 14(11P15.5) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 14(11P15.5) MUTATED   17  2  4  0
  DEL PEAK 14(11P15.5) WILD-TYPE 46  5  8  5
D32V9, multiclass
    clus
vv   DEL PEAK 14(11P15.5) MUTATED DEL PEAK 14(11P15.5) WILD-TYPE
  R0                           17                             46
  R1                            2                              5
  R2                            4                              8
  RX                            0                              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"
D32V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(11P15.5) MUTATED       0                         0    20
  DEL PEAK 14(11P15.5) WILD-TYPE     2                         1    56
D32V11, multiclass
                           clus
vv                          DEL PEAK 14(11P15.5) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               20
                           clus
vv                          DEL PEAK 14(11P15.5) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V12, binary
                                cls
clus                              0  1
  DEL PEAK 14(11P15.5) MUTATED    1  6
  DEL PEAK 14(11P15.5) WILD-TYPE  7 32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11P15.5) MUTATED      1    6
  DEL PEAK 14(11P15.5) WILD-TYPE    7   32
                        clus
vv                       DEL PEAK 14(11P15.5) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       DEL PEAK 14(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                             32
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK 15(11Q14.1) MUTATION ANALYSIS
D33V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 15(11Q14.1) MUTATED   17  7
  DEL PEAK 15(11Q14.1) WILD-TYPE 40 26
  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                            24                             66 
  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                             7                             26 
$`DEL PEAK 15(11Q14.1) MUTATED`
TCGA-PK-A5HB TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG 
       42.51        19.04        30.31        57.53        99.88        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV 
       69.37        76.64        49.22        36.26        12.59        66.51 
TCGA-OR-A5JW TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5L2 TCGA-OR-A5L6 
       72.39        49.08        11.31        24.36        60.89        28.31 
TCGA-OR-A5LC TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA 
        5.23        61.08        77.00        36.03        38.50        39.48 

$`DEL PEAK 15(11Q14.1) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J1 
       33.83        91.30        43.30        39.58        12.59        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        68.75        13.91        12.00        88.87        16.11 
TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL 
       44.45        18.12        69.21        66.25        16.11        67.59 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU 
       18.48        39.25        15.25       121.25        29.82         9.50 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       31.23        18.15        27.02       108.13        32.68       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS 
       35.57        16.37        24.62        46.49        88.01        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       95.18       153.63       127.50        68.25        44.84        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5L9 
        4.11        58.55       152.15        31.79        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH 
       23.64        39.35        21.76        14.63        52.24        78.41 
TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       14.33        36.33        90.08        53.03        79.07        61.05 
TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       28.04        18.05         0.00        24.85        20.25        22.32 

  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                          5.23                           0.00 
  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                         99.88                         153.63 
  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE 
                        40.995                         35.950 
[1] "5.2 - 99.9 (41.0)"  "0.0 - 153.6 (36.0)"
[1] "hr=" "1.3"
D33V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 15(11Q14.1) MUTATED         2       14         1        5
  DEL PEAK 15(11Q14.1) WILD-TYPE       7       29        17       13
D33V3, multiclass
           clus
vv          DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE
  STAGE I                              2                              7
  STAGE II                            14                             29
  STAGE III                            1                             17
  STAGE IV                             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"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 15(11Q14.1) MUTATED    2 15  1  4
  DEL PEAK 15(11Q14.1) WILD-TYPE  7 33 10 16
D33V4, multiclass
    clus
vv   DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE
  T1                            2                              7
  T2                           15                             33
  T3                            1                             10
  T4                            4                             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"
D33V5, binary
                                cls
clus                              0  1
  DEL PEAK 15(11Q14.1) MUTATED   20  2
  DEL PEAK 15(11Q14.1) WILD-TYPE 58  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q14.1) MUTATED     20    2
  DEL PEAK 15(11Q14.1) WILD-TYPE   58    8
   clus
vv  DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE
  0                           20                             58
  1                            2                              8
[1] 2 2
[1] FALSE
D33V6, binary
                                cls
clus                              0  1
  DEL PEAK 15(11Q14.1) MUTATED   13 11
  DEL PEAK 15(11Q14.1) WILD-TYPE 46 20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q14.1) MUTATED     13   11
  DEL PEAK 15(11Q14.1) WILD-TYPE   46   20
        clus
vv       DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE
  FEMALE                           13                             46
  MALE                             11                             20
[1] 2 2
[1] FALSE
D33V7, binary
                                cls
clus                              0  1
  DEL PEAK 15(11Q14.1) MUTATED   17  5
  DEL PEAK 15(11Q14.1) WILD-TYPE 52 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q14.1) MUTATED     17    5
  DEL PEAK 15(11Q14.1) WILD-TYPE   52   13
     clus
vv    DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE
  NO                            17                             52
  YES                            5                             13
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK 15(11Q14.1) MUTATED                                       1
  DEL PEAK 15(11Q14.1) WILD-TYPE                                     0
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK 15(11Q14.1) MUTATED                                          2
  DEL PEAK 15(11Q14.1) WILD-TYPE                                        2
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK 15(11Q14.1) MUTATED                                     21
  DEL PEAK 15(11Q14.1) WILD-TYPE                                   64
D33V8, multiclass
                                          clus
vv                                         DEL PEAK 15(11Q14.1) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               21
                                          clus
vv                                         DEL PEAK 15(11Q14.1) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 15(11Q14.1) MUTATED   17  2  2  0
  DEL PEAK 15(11Q14.1) WILD-TYPE 46  5 10  5
D33V9, multiclass
    clus
vv   DEL PEAK 15(11Q14.1) MUTATED DEL PEAK 15(11Q14.1) WILD-TYPE
  R0                           17                             46
  R1                            2                              5
  R2                            2                             10
  RX                            0                              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"
D33V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(11Q14.1) MUTATED       0                         0    19
  DEL PEAK 15(11Q14.1) WILD-TYPE     2                         1    57
D33V11, multiclass
                           clus
vv                          DEL PEAK 15(11Q14.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               19
                           clus
vv                          DEL PEAK 15(11Q14.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V12, binary
                                cls
clus                              0  1
  DEL PEAK 15(11Q14.1) MUTATED    1  6
  DEL PEAK 15(11Q14.1) WILD-TYPE  7 32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q14.1) MUTATED      1    6
  DEL PEAK 15(11Q14.1) WILD-TYPE    7   32
                        clus
vv                       DEL PEAK 15(11Q14.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            6
                        clus
vv                       DEL PEAK 15(11Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                             32
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK 16(12Q14.2) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 16(12Q14.2) MUTATED    1  4
  DEL PEAK 16(12Q14.2) WILD-TYPE 56 29
  DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE 
                             5                             85 
  DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE 
                             4                             29 
$`DEL PEAK 16(12Q14.2) MUTATED`
TCGA-P6-A5OG TCGA-OR-A5JB TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5LL 
       12.59        18.12        11.31        95.18        53.03 

$`DEL PEAK 16(12Q14.2) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        43.30        39.58        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        68.75        13.91        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       19.04        44.45        30.31        57.53        99.88        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       66.25        17.79        69.37        76.64        16.11        49.22 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       67.59        18.48        39.25        15.25        36.26       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        29.82         9.50        66.51        72.39        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
       18.15        27.02       108.13        32.68       113.92        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ 
       16.37        49.08        24.62        24.36        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       83.80       153.63       127.50        68.25        44.84        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
        4.11        58.55        60.89       152.15        31.79        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       29.10        28.64        23.64         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK 
       14.63        52.24        78.41        14.33        36.33        90.08 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        77.00        79.07        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       18.05        38.50         0.00        24.85        20.25        39.48 
TCGA-PK-A5HC 
       22.32 

  DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE 
                         11.31                           0.00 
  DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE 
                         95.18                         153.63 
  DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE 
                         18.12                          39.25 
[1] "11.3 - 95.2 (18.1)" "0.0 - 153.6 (39.2)"
[1] "hr=" "3"  
D34V2, 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       8       41        18       16
D34V3, multiclass
           clus
vv          DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE
  STAGE I                              1                              8
  STAGE II                             2                             41
  STAGE III                            0                             18
  STAGE IV                             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"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 16(12Q14.2) MUTATED    1  2  0  2
  DEL PEAK 16(12Q14.2) WILD-TYPE  8 46 11 18
D34V4, multiclass
    clus
vv   DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE
  T1                            1                              8
  T2                            2                             46
  T3                            0                             11
  T4                            2                             18
[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 16(12Q14.2) MUTATED    5  0
  DEL PEAK 16(12Q14.2) WILD-TYPE 73 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(12Q14.2) MUTATED      5    0
  DEL PEAK 16(12Q14.2) WILD-TYPE   73   10
   clus
vv  DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE
  0                            5                             73
  1                            0                             10
[1] 2 2
[1] FALSE
D34V6, binary
                                cls
clus                              0  1
  DEL PEAK 16(12Q14.2) MUTATED    4  1
  DEL PEAK 16(12Q14.2) WILD-TYPE 55 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(12Q14.2) MUTATED      4    1
  DEL PEAK 16(12Q14.2) WILD-TYPE   55   30
        clus
vv       DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE
  FEMALE                            4                             55
  MALE                              1                             30
[1] 2 2
[1] FALSE
D34V7, binary
                                cls
clus                              0  1
  DEL PEAK 16(12Q14.2) MUTATED    4  0
  DEL PEAK 16(12Q14.2) WILD-TYPE 65 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(12Q14.2) MUTATED      4    0
  DEL PEAK 16(12Q14.2) WILD-TYPE   65   18
     clus
vv    DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE
  NO                             4                             65
  YES                            0                             18
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK 16(12Q14.2) MUTATED                                       0
  DEL PEAK 16(12Q14.2) WILD-TYPE                                     1
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK 16(12Q14.2) MUTATED                                          0
  DEL PEAK 16(12Q14.2) WILD-TYPE                                        4
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK 16(12Q14.2) MUTATED                                      5
  DEL PEAK 16(12Q14.2) WILD-TYPE                                   80
D34V8, multiclass
                                          clus
vv                                         DEL PEAK 16(12Q14.2) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                5
                                          clus
vv                                         DEL PEAK 16(12Q14.2) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 16(12Q14.2) MUTATED    3  1  1  0
  DEL PEAK 16(12Q14.2) WILD-TYPE 60  6 11  5
D34V9, multiclass
    clus
vv   DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE
  R0                            3                             60
  R1                            1                              6
  R2                            1                             11
  RX                            0                              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"
D34V10, continuous
[1] "Remove cluster labels:"       "DEL PEAK 16(12Q14.2) MUTATED"
clus
  DEL PEAK 16(12Q14.2) MUTATED DEL PEAK 16(12Q14.2) WILD-TYPE 
                             2                             29 
                    TCGA-OR-A5KP                     TCGA-OR-A5J2 
"DEL PEAK 16(12Q14.2) WILD-TYPE" "DEL PEAK 16(12Q14.2) WILD-TYPE" 
                    TCGA-OR-A5J3                     TCGA-OR-A5J4 
"DEL PEAK 16(12Q14.2) WILD-TYPE" "DEL PEAK 16(12Q14.2) WILD-TYPE" 
                    TCGA-OR-A5J7                     TCGA-OR-A5J8 
"DEL PEAK 16(12Q14.2) WILD-TYPE" "DEL PEAK 16(12Q14.2) WILD-TYPE" 
                    TCGA-OR-A5JG                     TCGA-OR-A5JJ 
"DEL PEAK 16(12Q14.2) WILD-TYPE" "DEL PEAK 16(12Q14.2) WILD-TYPE" 
                    TCGA-OR-A5JT                     TCGA-OR-A5JV 
"DEL PEAK 16(12Q14.2) WILD-TYPE" "DEL PEAK 16(12Q14.2) WILD-TYPE" 
                    TCGA-OR-A5JX                     TCGA-OR-A5JY 
"DEL PEAK 16(12Q14.2) WILD-TYPE" "DEL PEAK 16(12Q14.2) WILD-TYPE" 
                    TCGA-OR-A5K2                     TCGA-OR-A5K5 
"DEL PEAK 16(12Q14.2) WILD-TYPE" "DEL PEAK 16(12Q14.2) WILD-TYPE" 
                    TCGA-OR-A5KB                     TCGA-OR-A5KU 
"DEL PEAK 16(12Q14.2) WILD-TYPE" "DEL PEAK 16(12Q14.2) WILD-TYPE" 
                    TCGA-OR-A5KV                     TCGA-OR-A5KW 
"DEL PEAK 16(12Q14.2) WILD-TYPE" "DEL PEAK 16(12Q14.2) WILD-TYPE" 
                    TCGA-OR-A5KY                     TCGA-OR-A5L9 
"DEL PEAK 16(12Q14.2) WILD-TYPE" "DEL PEAK 16(12Q14.2) WILD-TYPE" 
                    TCGA-OR-A5LG                     TCGA-OR-A5LM 
"DEL PEAK 16(12Q14.2) WILD-TYPE" "DEL PEAK 16(12Q14.2) WILD-TYPE" 
                    TCGA-OR-A5LN                     TCGA-OR-A5LO 
"DEL PEAK 16(12Q14.2) WILD-TYPE" "DEL PEAK 16(12Q14.2) WILD-TYPE" 
                    TCGA-OR-A5LP                     TCGA-OR-A5LT 
"DEL PEAK 16(12Q14.2) WILD-TYPE" "DEL PEAK 16(12Q14.2) WILD-TYPE" 
                    TCGA-OU-A5PI                     TCGA-PK-A5HA 
"DEL PEAK 16(12Q14.2) WILD-TYPE" "DEL PEAK 16(12Q14.2) WILD-TYPE" 
                    TCGA-PK-A5HC 
"DEL PEAK 16(12Q14.2) WILD-TYPE" 
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(12Q14.2) MUTATED       0                         0     4
  DEL PEAK 16(12Q14.2) WILD-TYPE     2                         1    72
D34V11, multiclass
                           clus
vv                          DEL PEAK 16(12Q14.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                4
                           clus
vv                          DEL PEAK 16(12Q14.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V12, binary
                                cls
clus                              0  1
  DEL PEAK 16(12Q14.2) MUTATED    0  2
  DEL PEAK 16(12Q14.2) WILD-TYPE  8 36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(12Q14.2) MUTATED      0    2
  DEL PEAK 16(12Q14.2) WILD-TYPE    8   36
                        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                             36
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 17(13Q14.2) MUTATION ANALYSIS
D35V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 17(13Q14.2) MUTATED   23 19
  DEL PEAK 17(13Q14.2) WILD-TYPE 34 14
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                            42                             48 
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                            19                             14 
$`DEL PEAK 17(13Q14.2) MUTATED`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J4 TCGA-OR-A5J7 
       33.83        91.30        12.59        42.51        13.91        16.11 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JG 
       30.31        18.12        57.53        99.88        69.21        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JS 
       69.37        76.64        49.22        15.25        36.26        12.59 
TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 
        9.50        66.51        72.39        18.15        32.68        16.37 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KZ 
       11.31        24.36        46.49        83.80       153.63         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L6 TCGA-OR-A5LD TCGA-OR-A5LI TCGA-OR-A5LK 
       58.55        60.89        28.31        39.35        14.33        90.08 
TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PK-A5HA 
       53.03        77.00        36.03        38.50         0.00        39.48 

$`DEL PEAK 17(13Q14.2) WILD-TYPE`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 
       43.30        39.58        44.55        55.13        68.75        12.00 
TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL 
       88.87        19.04        44.45        66.25        16.11        67.59 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JX TCGA-OR-A5JZ 
       18.48        39.25       121.25        29.82        31.23        27.02 
TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KQ 
      108.13       113.92        35.57        49.08        24.62        88.01 
TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L3 
       95.18       127.50        68.25        44.84        12.85       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LE 
       31.79        29.10        28.64        23.64         5.23        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LM TCGA-OR-A5LO 
       14.63        52.24        78.41        36.33        61.08        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       61.05        28.04        18.05        24.85        20.25        22.32 

  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                          0.00                           5.23 
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                        153.63                         152.15 
  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE 
                        37.380                         39.415 
[1] "0.0 - 153.6 (37.4)" "5.2 - 152.2 (39.4)"
[1] "hr=" "1.8"
D35V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 17(13Q14.2) MUTATED         3       21         5       11
  DEL PEAK 17(13Q14.2) WILD-TYPE       6       22        13        7
D35V3, multiclass
           clus
vv          DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE
  STAGE I                              3                              6
  STAGE II                            21                             22
  STAGE III                            5                             13
  STAGE IV                            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"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 17(13Q14.2) MUTATED    3 22  4 11
  DEL PEAK 17(13Q14.2) WILD-TYPE  6 26  7  9
D35V4, multiclass
    clus
vv   DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE
  T1                            3                              6
  T2                           22                             26
  T3                            4                              7
  T4                           11                              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"
D35V5, binary
                                cls
clus                              0  1
  DEL PEAK 17(13Q14.2) MUTATED   36  4
  DEL PEAK 17(13Q14.2) WILD-TYPE 42  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(13Q14.2) MUTATED     36    4
  DEL PEAK 17(13Q14.2) WILD-TYPE   42    6
   clus
vv  DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE
  0                           36                             42
  1                            4                              6
[1] 2 2
[1] FALSE
D35V6, binary
                                cls
clus                              0  1
  DEL PEAK 17(13Q14.2) MUTATED   27 15
  DEL PEAK 17(13Q14.2) WILD-TYPE 32 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(13Q14.2) MUTATED     27   15
  DEL PEAK 17(13Q14.2) WILD-TYPE   32   16
        clus
vv       DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE
  FEMALE                           27                             32
  MALE                             15                             16
[1] 2 2
[1] FALSE
D35V7, binary
                                cls
clus                              0  1
  DEL PEAK 17(13Q14.2) MUTATED   31  8
  DEL PEAK 17(13Q14.2) WILD-TYPE 38 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(13Q14.2) MUTATED     31    8
  DEL PEAK 17(13Q14.2) WILD-TYPE   38   10
     clus
vv    DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE
  NO                            31                             38
  YES                            8                             10
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK 17(13Q14.2) MUTATED                                       1
  DEL PEAK 17(13Q14.2) WILD-TYPE                                     0
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK 17(13Q14.2) MUTATED                                          3
  DEL PEAK 17(13Q14.2) WILD-TYPE                                        1
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK 17(13Q14.2) MUTATED                                     38
  DEL PEAK 17(13Q14.2) WILD-TYPE                                   47
D35V8, multiclass
                                          clus
vv                                         DEL PEAK 17(13Q14.2) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            3
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               38
                                          clus
vv                                         DEL PEAK 17(13Q14.2) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              1
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 17(13Q14.2) MUTATED   27  4  6  2
  DEL PEAK 17(13Q14.2) WILD-TYPE 36  3  6  3
D35V9, multiclass
    clus
vv   DEL PEAK 17(13Q14.2) MUTATED DEL PEAK 17(13Q14.2) WILD-TYPE
  R0                           27                             36
  R1                            4                              3
  R2                            6                              6
  RX                            2                              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"
D35V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(13Q14.2) MUTATED       0                         0    36
  DEL PEAK 17(13Q14.2) WILD-TYPE     2                         1    40
D35V11, multiclass
                           clus
vv                          DEL PEAK 17(13Q14.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               36
                           clus
vv                          DEL PEAK 17(13Q14.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V12, binary
                                cls
clus                              0  1
  DEL PEAK 17(13Q14.2) MUTATED    2 14
  DEL PEAK 17(13Q14.2) WILD-TYPE  6 24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(13Q14.2) MUTATED      2   14
  DEL PEAK 17(13Q14.2) WILD-TYPE    6   24
                        clus
vv                       DEL PEAK 17(13Q14.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           14
                        clus
vv                       DEL PEAK 17(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             24
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 18(14Q21.2) MUTATION ANALYSIS
D36V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(14Q21.2) MUTATED   14  6
  DEL PEAK 18(14Q21.2) WILD-TYPE 43 27
  DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE 
                            20                             70 
  DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE 
                             6                             27 
$`DEL PEAK 18(14Q21.2) MUTATED`
TCGA-P6-A5OG TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JC TCGA-OR-A5JD 
       12.59        88.87        16.11        19.04        57.53        99.88 
TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5KB TCGA-OR-A5KO 
       69.37        49.22        36.26        66.51        24.36        46.49 
TCGA-OR-A5KQ TCGA-OR-A5KZ TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LN TCGA-OR-A5LS 
       88.01         4.11        28.31         5.23        77.00        36.03 
TCGA-OR-A5LT TCGA-PK-A5HA 
       18.05        39.48 

$`DEL PEAK 18(14Q21.2) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 
       33.83        91.30        43.30        39.58        42.51        44.55 
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JA 
       55.13        68.75        13.91        12.00        44.45        30.31 
TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JJ 
       18.12        69.21        66.25        17.79        76.64        16.11 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS 
       67.59        18.48        39.25        15.25       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ 
       29.82         9.50        72.39        31.23        18.15        27.02 
TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
      108.13        32.68       113.92        35.57        16.37        49.08 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       24.62        11.31        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       68.25        44.84        12.85        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LE 
       31.79        29.10        28.64        23.64        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK 
       14.63        52.24        78.41        14.33        36.33        90.08 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OU-A5PI 
       53.03        61.08        79.07        61.05        28.04        38.50 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
        0.00        24.85        20.25        22.32 

  DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE 
                          4.11                           0.00 
  DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE 
                         99.88                         153.63 
  DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE 
                        37.870                         38.875 
[1] "4.1 - 99.9 (37.9)"  "0.0 - 153.6 (38.9)"
[1] "hr=" "1.3"
D36V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 18(14Q21.2) MUTATED         1       11         3        4
  DEL PEAK 18(14Q21.2) WILD-TYPE       8       32        15       14
D36V3, multiclass
           clus
vv          DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE
  STAGE I                              1                              8
  STAGE II                            11                             32
  STAGE III                            3                             15
  STAGE IV                             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"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 18(14Q21.2) MUTATED    1 11  3  4
  DEL PEAK 18(14Q21.2) WILD-TYPE  8 37  8 16
D36V4, multiclass
    clus
vv   DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE
  T1                            1                              8
  T2                           11                             37
  T3                            3                              8
  T4                            4                             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"
D36V5, binary
                                cls
clus                              0  1
  DEL PEAK 18(14Q21.2) MUTATED   19  0
  DEL PEAK 18(14Q21.2) WILD-TYPE 59 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(14Q21.2) MUTATED     19    0
  DEL PEAK 18(14Q21.2) WILD-TYPE   59   10
   clus
vv  DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE
  0                           19                             59
  1                            0                             10
[1] 2 2
[1] FALSE
D36V6, binary
                                cls
clus                              0  1
  DEL PEAK 18(14Q21.2) MUTATED   12  8
  DEL PEAK 18(14Q21.2) WILD-TYPE 47 23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(14Q21.2) MUTATED     12    8
  DEL PEAK 18(14Q21.2) WILD-TYPE   47   23
        clus
vv       DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE
  FEMALE                           12                             47
  MALE                              8                             23
[1] 2 2
[1] FALSE
D36V7, binary
                                cls
clus                              0  1
  DEL PEAK 18(14Q21.2) MUTATED   17  2
  DEL PEAK 18(14Q21.2) WILD-TYPE 52 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(14Q21.2) MUTATED     17    2
  DEL PEAK 18(14Q21.2) WILD-TYPE   52   16
     clus
vv    DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE
  NO                            17                             52
  YES                            2                             16
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK 18(14Q21.2) MUTATED                                       1
  DEL PEAK 18(14Q21.2) WILD-TYPE                                     0
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK 18(14Q21.2) MUTATED                                          2
  DEL PEAK 18(14Q21.2) WILD-TYPE                                        2
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK 18(14Q21.2) MUTATED                                     17
  DEL PEAK 18(14Q21.2) WILD-TYPE                                   68
D36V8, multiclass
                                          clus
vv                                         DEL PEAK 18(14Q21.2) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               17
                                          clus
vv                                         DEL PEAK 18(14Q21.2) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 18(14Q21.2) MUTATED   14  1  3  1
  DEL PEAK 18(14Q21.2) WILD-TYPE 49  6  9  4
D36V9, multiclass
    clus
vv   DEL PEAK 18(14Q21.2) MUTATED DEL PEAK 18(14Q21.2) WILD-TYPE
  R0                           14                             49
  R1                            1                              6
  R2                            3                              9
  RX                            1                              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"
D36V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(14Q21.2) MUTATED       0                         1    15
  DEL PEAK 18(14Q21.2) WILD-TYPE     2                         0    61
D36V11, multiclass
                           clus
vv                          DEL PEAK 18(14Q21.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               15
                           clus
vv                          DEL PEAK 18(14Q21.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V12, binary
                                cls
clus                              0  1
  DEL PEAK 18(14Q21.2) MUTATED    3  7
  DEL PEAK 18(14Q21.2) WILD-TYPE  5 31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(14Q21.2) MUTATED      3    7
  DEL PEAK 18(14Q21.2) WILD-TYPE    5   31
                        clus
vv                       DEL PEAK 18(14Q21.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                            7
                        clus
vv                       DEL PEAK 18(14Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                             31
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 19(15Q15.1) MUTATION ANALYSIS
D37V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 19(15Q15.1) MUTATED   15 10
  DEL PEAK 19(15Q15.1) WILD-TYPE 42 23
  DEL PEAK 19(15Q15.1) MUTATED DEL PEAK 19(15Q15.1) WILD-TYPE 
                            25                             65 
  DEL PEAK 19(15Q15.1) MUTATED DEL PEAK 19(15Q15.1) WILD-TYPE 
                            10                             23 
$`DEL PEAK 19(15Q15.1) MUTATED`
TCGA-OR-A5KP TCGA-P6-A5OG TCGA-OR-A5J7 TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI 
       91.30        12.59        16.11        99.88        69.37        76.64 
TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5K2 
       18.48        15.25        36.26        66.51        31.23        32.68 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KX TCGA-OR-A5L2 TCGA-OR-A5L6 
       16.37        11.31        95.18        44.84        60.89        28.31 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
        5.23        39.35        36.03        18.05        38.50         0.00 
TCGA-PK-A5HA 
       39.48 

$`DEL PEAK 19(15Q15.1) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       33.83        43.30        39.58        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 
       68.75        13.91        12.00        88.87        19.04        44.45 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       30.31        18.12        57.53        69.21        66.25        17.79 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5JS 
       16.11        49.22        67.59        39.25       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 
       29.82         9.50        72.39        18.15        27.02       108.13 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO 
      113.92        35.57        49.08        24.62        24.36        46.49 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY 
       88.01        83.80       153.63       127.50        68.25        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5L9 
        4.11        58.55       152.15        31.79        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI 
       23.64        21.76        14.63        52.24        78.41        14.33 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO 
       36.33        90.08        53.03        61.08        77.00        79.07 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       61.05        28.04        24.85        20.25        22.32 

  DEL PEAK 19(15Q15.1) MUTATED DEL PEAK 19(15Q15.1) WILD-TYPE 
                          0.00                           4.11 
  DEL PEAK 19(15Q15.1) MUTATED DEL PEAK 19(15Q15.1) WILD-TYPE 
                         99.88                         153.63 
  DEL PEAK 19(15Q15.1) MUTATED DEL PEAK 19(15Q15.1) WILD-TYPE 
                         36.03                          42.51 
[1] "0.0 - 99.9 (36.0)"  "4.1 - 153.6 (42.5)"
[1] "hr=" "1.3"
D37V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 19(15Q15.1) MUTATED         3       10         7        5
  DEL PEAK 19(15Q15.1) WILD-TYPE       6       33        11       13
D37V3, multiclass
           clus
vv          DEL PEAK 19(15Q15.1) MUTATED DEL PEAK 19(15Q15.1) WILD-TYPE
  STAGE I                              3                              6
  STAGE II                            10                             33
  STAGE III                            7                             11
  STAGE IV                             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"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 19(15Q15.1) MUTATED    3 12  4  6
  DEL PEAK 19(15Q15.1) WILD-TYPE  6 36  7 14
D37V4, multiclass
    clus
vv   DEL PEAK 19(15Q15.1) MUTATED DEL PEAK 19(15Q15.1) WILD-TYPE
  T1                            3                              6
  T2                           12                             36
  T3                            4                              7
  T4                            6                             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 19(15Q15.1) MUTATED   23  2
  DEL PEAK 19(15Q15.1) WILD-TYPE 55  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(15Q15.1) MUTATED     23    2
  DEL PEAK 19(15Q15.1) WILD-TYPE   55    8
   clus
vv  DEL PEAK 19(15Q15.1) MUTATED DEL PEAK 19(15Q15.1) WILD-TYPE
  0                           23                             55
  1                            2                              8
[1] 2 2
[1] FALSE
D37V6, binary
                                cls
clus                              0  1
  DEL PEAK 19(15Q15.1) MUTATED   17  8
  DEL PEAK 19(15Q15.1) WILD-TYPE 42 23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(15Q15.1) MUTATED     17    8
  DEL PEAK 19(15Q15.1) WILD-TYPE   42   23
        clus
vv       DEL PEAK 19(15Q15.1) MUTATED DEL PEAK 19(15Q15.1) WILD-TYPE
  FEMALE                           17                             42
  MALE                              8                             23
[1] 2 2
[1] FALSE
D37V7, binary
                                cls
clus                              0  1
  DEL PEAK 19(15Q15.1) MUTATED   21  4
  DEL PEAK 19(15Q15.1) WILD-TYPE 48 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(15Q15.1) MUTATED     21    4
  DEL PEAK 19(15Q15.1) WILD-TYPE   48   14
     clus
vv    DEL PEAK 19(15Q15.1) MUTATED DEL PEAK 19(15Q15.1) WILD-TYPE
  NO                            21                             48
  YES                            4                             14
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK 19(15Q15.1) MUTATED                                       1
  DEL PEAK 19(15Q15.1) WILD-TYPE                                     0
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK 19(15Q15.1) MUTATED                                          2
  DEL PEAK 19(15Q15.1) WILD-TYPE                                        2
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK 19(15Q15.1) MUTATED                                     22
  DEL PEAK 19(15Q15.1) WILD-TYPE                                   63
D37V8, multiclass
                                          clus
vv                                         DEL PEAK 19(15Q15.1) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               22
                                          clus
vv                                         DEL PEAK 19(15Q15.1) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 19(15Q15.1) MUTATED   18  2  3  1
  DEL PEAK 19(15Q15.1) WILD-TYPE 45  5  9  4
D37V9, multiclass
    clus
vv   DEL PEAK 19(15Q15.1) MUTATED DEL PEAK 19(15Q15.1) WILD-TYPE
  R0                           18                             45
  R1                            2                              5
  R2                            3                              9
  RX                            1                              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"
D37V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(15Q15.1) MUTATED       0                         0    22
  DEL PEAK 19(15Q15.1) WILD-TYPE     2                         1    54
D37V11, multiclass
                           clus
vv                          DEL PEAK 19(15Q15.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               22
                           clus
vv                          DEL PEAK 19(15Q15.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V12, binary
                                cls
clus                              0  1
  DEL PEAK 19(15Q15.1) MUTATED    1 10
  DEL PEAK 19(15Q15.1) WILD-TYPE  7 28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(15Q15.1) MUTATED      1   10
  DEL PEAK 19(15Q15.1) WILD-TYPE    7   28
                        clus
vv                       DEL PEAK 19(15Q15.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           10
                        clus
vv                       DEL PEAK 19(15Q15.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                             28
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 20(16P13.3) MUTATION ANALYSIS
D38V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 20(16P13.3) MUTATED    3  5
  DEL PEAK 20(16P13.3) WILD-TYPE 54 28
  DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE 
                             8                             82 
  DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE 
                             5                             28 
$`DEL PEAK 20(16P13.3) MUTATED`
TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JY 
       39.58        12.59        88.87        16.11        18.12        18.15 
TCGA-OR-A5LG TCGA-OR-A5LS 
       52.24        36.03 

$`DEL PEAK 20(16P13.3) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 
       33.83        91.30        43.30        42.51        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA 
       68.75        13.91        12.00        19.04        44.45        30.31 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH 
       57.53        99.88        69.21        66.25        17.79        69.37 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       76.64        16.11        49.22        67.59        18.48        39.25 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU 
       15.25        36.26       121.25        12.59        29.82         9.50 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 
       66.51        72.39        31.23        27.02       108.13        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 
      113.92        35.57        16.37        49.08        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       24.36        46.49        88.01        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      127.50        68.25        44.84        12.85         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
       60.89       152.15        31.79        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LH 
       23.64         5.23        39.35        21.76        14.63        78.41 
TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       14.33        36.33        90.08        53.03        61.08        77.00 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       79.07        61.05        28.04        18.05        38.50         0.00 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       24.85        20.25        39.48        22.32 

  DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE 
                         12.59                           0.00 
  DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE 
                         88.87                         153.63 
  DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE 
                         27.09                          39.30 
[1] "12.6 - 88.9 (27.1)" "0.0 - 153.6 (39.3)"
[1] "hr=" "2.3"
D38V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 20(16P13.3) MUTATED         0        2         2        4
  DEL PEAK 20(16P13.3) WILD-TYPE       9       41        16       14
D38V3, multiclass
           clus
vv          DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE
  STAGE I                              0                              9
  STAGE II                             2                             41
  STAGE III                            2                             16
  STAGE IV                             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"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 20(16P13.3) MUTATED    0  2  2  4
  DEL PEAK 20(16P13.3) WILD-TYPE  9 46  9 16
D38V4, multiclass
    clus
vv   DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE
  T1                            0                              9
  T2                            2                             46
  T3                            2                              9
  T4                            4                             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"
D38V5, binary
                                cls
clus                              0  1
  DEL PEAK 20(16P13.3) MUTATED    7  1
  DEL PEAK 20(16P13.3) WILD-TYPE 71  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(16P13.3) MUTATED      7    1
  DEL PEAK 20(16P13.3) WILD-TYPE   71    9
   clus
vv  DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE
  0                            7                             71
  1                            1                              9
[1] 2 2
[1] FALSE
D38V6, binary
                                cls
clus                              0  1
  DEL PEAK 20(16P13.3) MUTATED    5  3
  DEL PEAK 20(16P13.3) WILD-TYPE 54 28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(16P13.3) MUTATED      5    3
  DEL PEAK 20(16P13.3) WILD-TYPE   54   28
        clus
vv       DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE
  FEMALE                            5                             54
  MALE                              3                             28
[1] 2 2
[1] FALSE
D38V7, binary
                                cls
clus                              0  1
  DEL PEAK 20(16P13.3) MUTATED    5  2
  DEL PEAK 20(16P13.3) WILD-TYPE 64 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(16P13.3) MUTATED      5    2
  DEL PEAK 20(16P13.3) WILD-TYPE   64   16
     clus
vv    DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE
  NO                             5                             64
  YES                            2                             16
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK 20(16P13.3) MUTATED                                       0
  DEL PEAK 20(16P13.3) WILD-TYPE                                     1
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK 20(16P13.3) MUTATED                                          0
  DEL PEAK 20(16P13.3) WILD-TYPE                                        4
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK 20(16P13.3) MUTATED                                      8
  DEL PEAK 20(16P13.3) WILD-TYPE                                   77
D38V8, multiclass
                                          clus
vv                                         DEL PEAK 20(16P13.3) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                8
                                          clus
vv                                         DEL PEAK 20(16P13.3) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 20(16P13.3) MUTATED    3  2  2  1
  DEL PEAK 20(16P13.3) WILD-TYPE 60  5 10  4
D38V9, multiclass
    clus
vv   DEL PEAK 20(16P13.3) MUTATED DEL PEAK 20(16P13.3) WILD-TYPE
  R0                            3                             60
  R1                            2                              5
  R2                            2                             10
  RX                            1                              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"
D38V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(16P13.3) MUTATED       0                         1     6
  DEL PEAK 20(16P13.3) WILD-TYPE     2                         0    70
D38V11, multiclass
                           clus
vv                          DEL PEAK 20(16P13.3) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                                6
                           clus
vv                          DEL PEAK 20(16P13.3) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V12, binary
                                cls
clus                              0  1
  DEL PEAK 20(16P13.3) MUTATED    2  3
  DEL PEAK 20(16P13.3) WILD-TYPE  6 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(16P13.3) MUTATED      2    3
  DEL PEAK 20(16P13.3) WILD-TYPE    6   35
                        clus
vv                       DEL PEAK 20(16P13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                            3
                        clus
vv                       DEL PEAK 20(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             35
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 21(16Q23.1) MUTATION ANALYSIS
D39V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 21(16Q23.1) MUTATED    3  8
  DEL PEAK 21(16Q23.1) WILD-TYPE 54 25
  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                            11                             79 
  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                             8                             25 
$`DEL PEAK 21(16Q23.1) MUTATED`
TCGA-OR-A5K0 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5KB 
       33.83        39.58        12.59        16.11        18.12        24.36 
TCGA-OR-A5L2 TCGA-OR-A5LD TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LL 
       60.89        39.35        52.24        14.33        53.03 

$`DEL PEAK 21(16Q23.1) WILD-TYPE`
TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       91.30        43.30        42.51        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA 
       13.91        12.00        88.87        19.04        44.45        30.31 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH 
       57.53        99.88        69.21        66.25        17.79        69.37 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       76.64        16.11        49.22        67.59        18.48        39.25 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU 
       15.25        36.26       121.25        12.59        29.82         9.50 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 
       66.51        72.39        31.23        18.15        27.02       108.13 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 
       32.68       113.92        35.57        16.37        49.08        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        46.49        88.01        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      127.50        68.25        44.84        12.85         4.11        58.55 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        28.31        29.10        28.64        23.64 
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        90.08 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        77.00        79.07        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       18.05        38.50         0.00        24.85        20.25        39.48 
TCGA-PK-A5HC 
       22.32 

  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                         12.59                           0.00 
  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                         60.89                         153.63 
  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                         33.83                          39.25 
[1] "12.6 - 60.9 (33.8)" "0.0 - 153.6 (39.2)"
[1] "hr=" "3.2"
D39V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 21(16Q23.1) MUTATED         0        4         3        4
  DEL PEAK 21(16Q23.1) WILD-TYPE       9       39        15       14
D39V3, multiclass
           clus
vv          DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE
  STAGE I                              0                              9
  STAGE II                             4                             39
  STAGE III                            3                             15
  STAGE IV                             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"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 21(16Q23.1) MUTATED    0  4  2  5
  DEL PEAK 21(16Q23.1) WILD-TYPE  9 44  9 15
D39V4, multiclass
    clus
vv   DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE
  T1                            0                              9
  T2                            4                             44
  T3                            2                              9
  T4                            5                             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 21(16Q23.1) MUTATED   11  0
  DEL PEAK 21(16Q23.1) WILD-TYPE 67 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(16Q23.1) MUTATED     11    0
  DEL PEAK 21(16Q23.1) WILD-TYPE   67   10
   clus
vv  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE
  0                           11                             67
  1                            0                             10
[1] 2 2
[1] FALSE
D39V6, binary
                                cls
clus                              0  1
  DEL PEAK 21(16Q23.1) MUTATED    7  4
  DEL PEAK 21(16Q23.1) WILD-TYPE 52 27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(16Q23.1) MUTATED      7    4
  DEL PEAK 21(16Q23.1) WILD-TYPE   52   27
        clus
vv       DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE
  FEMALE                            7                             52
  MALE                              4                             27
[1] 2 2
[1] FALSE
D39V7, binary
                                cls
clus                              0  1
  DEL PEAK 21(16Q23.1) MUTATED    9  1
  DEL PEAK 21(16Q23.1) WILD-TYPE 60 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(16Q23.1) MUTATED      9    1
  DEL PEAK 21(16Q23.1) WILD-TYPE   60   17
     clus
vv    DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE
  NO                             9                             60
  YES                            1                             17
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK 21(16Q23.1) MUTATED                                       0
  DEL PEAK 21(16Q23.1) WILD-TYPE                                     1
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK 21(16Q23.1) MUTATED                                          0
  DEL PEAK 21(16Q23.1) WILD-TYPE                                        4
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK 21(16Q23.1) MUTATED                                     11
  DEL PEAK 21(16Q23.1) WILD-TYPE                                   74
D39V8, multiclass
                                          clus
vv                                         DEL PEAK 21(16Q23.1) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               11
                                          clus
vv                                         DEL PEAK 21(16Q23.1) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 21(16Q23.1) MUTATED    5  2  2  2
  DEL PEAK 21(16Q23.1) WILD-TYPE 58  5 10  3
D39V9, multiclass
    clus
vv   DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE
  R0                            5                             58
  R1                            2                              5
  R2                            2                             10
  RX                            2                              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"
D39V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(16Q23.1) MUTATED       0                         0    10
  DEL PEAK 21(16Q23.1) WILD-TYPE     2                         1    66
D39V11, multiclass
                           clus
vv                          DEL PEAK 21(16Q23.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               10
                           clus
vv                          DEL PEAK 21(16Q23.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V12, binary
                                cls
clus                              0  1
  DEL PEAK 21(16Q23.1) MUTATED    1  7
  DEL PEAK 21(16Q23.1) WILD-TYPE  7 31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(16Q23.1) MUTATED      1    7
  DEL PEAK 21(16Q23.1) WILD-TYPE    7   31
                        clus
vv                       DEL PEAK 21(16Q23.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            7
                        clus
vv                       DEL PEAK 21(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                             31
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 22(17Q11.2) MUTATION ANALYSIS
D40V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 22(17Q11.2) MUTATED   12 12
  DEL PEAK 22(17Q11.2) WILD-TYPE 45 21
  DEL PEAK 22(17Q11.2) MUTATED DEL PEAK 22(17Q11.2) WILD-TYPE 
                            24                             66 
  DEL PEAK 22(17Q11.2) MUTATED DEL PEAK 22(17Q11.2) WILD-TYPE 
                            12                             21 
$`DEL PEAK 22(17Q11.2) MUTATED`
TCGA-OR-A5KP TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB 
       91.30        12.59        42.51        16.11        30.31        18.12 
TCGA-OR-A5JC TCGA-OR-A5JG TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JV 
       57.53        17.79        49.22        15.25        12.59        66.51 
TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5K9 TCGA-OR-A5KY TCGA-OR-A5L6 TCGA-OR-A5LC 
       72.39        32.68        11.31        12.85        28.31         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LM TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA 
       39.35        21.76        61.08        36.03        38.50        39.48 

$`DEL PEAK 22(17Q11.2) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       33.83        43.30        39.58        44.55        55.13        68.75 
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JD 
       13.91        12.00        88.87        19.04        44.45        99.88 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL 
       69.21        66.25        69.37        76.64        16.11        67.59 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU 
       18.48        39.25        36.26       121.25        29.82         9.50 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 
       31.23        18.15        27.02       108.13       113.92        35.57 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ 
       16.37        49.08        24.62        24.36        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        68.25        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L8 
        4.11        58.55        60.89       152.15        31.79        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI 
       28.64        23.64        14.63        52.24        78.41        14.33 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP 
       36.33        90.08        53.03        77.00        79.07        61.05 
TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       28.04        18.05         0.00        24.85        20.25        22.32 

  DEL PEAK 22(17Q11.2) MUTATED DEL PEAK 22(17Q11.2) WILD-TYPE 
                          5.23                           0.00 
  DEL PEAK 22(17Q11.2) MUTATED DEL PEAK 22(17Q11.2) WILD-TYPE 
                         91.30                         153.63 
  DEL PEAK 22(17Q11.2) MUTATED DEL PEAK 22(17Q11.2) WILD-TYPE 
                        31.495                         43.875 
[1] "5.2 - 91.3 (31.5)"  "0.0 - 153.6 (43.9)"
[1] "hr=" "2.2"
D40V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 22(17Q11.2) MUTATED         1       10         3        8
  DEL PEAK 22(17Q11.2) WILD-TYPE       8       33        15       10
D40V3, multiclass
           clus
vv          DEL PEAK 22(17Q11.2) MUTATED DEL PEAK 22(17Q11.2) WILD-TYPE
  STAGE I                              1                              8
  STAGE II                            10                             33
  STAGE III                            3                             15
  STAGE IV                             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"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 22(17Q11.2) MUTATED    1 11  1  9
  DEL PEAK 22(17Q11.2) WILD-TYPE  8 37 10 11
D40V4, multiclass
    clus
vv   DEL PEAK 22(17Q11.2) MUTATED DEL PEAK 22(17Q11.2) WILD-TYPE
  T1                            1                              8
  T2                           11                             37
  T3                            1                             10
  T4                            9                             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"
D40V5, binary
                                cls
clus                              0  1
  DEL PEAK 22(17Q11.2) MUTATED   19  3
  DEL PEAK 22(17Q11.2) WILD-TYPE 59  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(17Q11.2) MUTATED     19    3
  DEL PEAK 22(17Q11.2) WILD-TYPE   59    7
   clus
vv  DEL PEAK 22(17Q11.2) MUTATED DEL PEAK 22(17Q11.2) WILD-TYPE
  0                           19                             59
  1                            3                              7
[1] 2 2
[1] FALSE
D40V6, binary
                                cls
clus                              0  1
  DEL PEAK 22(17Q11.2) MUTATED   11 13
  DEL PEAK 22(17Q11.2) WILD-TYPE 48 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(17Q11.2) MUTATED     11   13
  DEL PEAK 22(17Q11.2) WILD-TYPE   48   18
        clus
vv       DEL PEAK 22(17Q11.2) MUTATED DEL PEAK 22(17Q11.2) WILD-TYPE
  FEMALE                           11                             48
  MALE                             13                             18
[1] 2 2
[1] FALSE
D40V7, binary
                                cls
clus                              0  1
  DEL PEAK 22(17Q11.2) MUTATED   16  5
  DEL PEAK 22(17Q11.2) WILD-TYPE 53 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(17Q11.2) MUTATED     16    5
  DEL PEAK 22(17Q11.2) WILD-TYPE   53   13
     clus
vv    DEL PEAK 22(17Q11.2) MUTATED DEL PEAK 22(17Q11.2) WILD-TYPE
  NO                            16                             53
  YES                            5                             13
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK 22(17Q11.2) MUTATED                                       0
  DEL PEAK 22(17Q11.2) WILD-TYPE                                     1
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK 22(17Q11.2) MUTATED                                          0
  DEL PEAK 22(17Q11.2) WILD-TYPE                                        4
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK 22(17Q11.2) MUTATED                                     24
  DEL PEAK 22(17Q11.2) WILD-TYPE                                   61
D40V8, multiclass
                                          clus
vv                                         DEL PEAK 22(17Q11.2) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               24
                                          clus
vv                                         DEL PEAK 22(17Q11.2) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 22(17Q11.2) MUTATED   12  4  4  1
  DEL PEAK 22(17Q11.2) WILD-TYPE 51  3  8  4
D40V9, multiclass
    clus
vv   DEL PEAK 22(17Q11.2) MUTATED DEL PEAK 22(17Q11.2) WILD-TYPE
  R0                           12                             51
  R1                            4                              3
  R2                            4                              8
  RX                            1                              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"
D40V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(17Q11.2) MUTATED       0                         0    20
  DEL PEAK 22(17Q11.2) WILD-TYPE     2                         1    56
D40V11, multiclass
                           clus
vv                          DEL PEAK 22(17Q11.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               20
                           clus
vv                          DEL PEAK 22(17Q11.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V12, binary
                                cls
clus                              0  1
  DEL PEAK 22(17Q11.2) MUTATED    1  8
  DEL PEAK 22(17Q11.2) WILD-TYPE  7 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(17Q11.2) MUTATED      1    8
  DEL PEAK 22(17Q11.2) WILD-TYPE    7   30
                        clus
vv                       DEL PEAK 22(17Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            8
                        clus
vv                       DEL PEAK 22(17Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                             30
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 23(17Q21.2) MUTATION ANALYSIS
D41V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 23(17Q21.2) MUTATED   12 14
  DEL PEAK 23(17Q21.2) WILD-TYPE 45 19
  DEL PEAK 23(17Q21.2) MUTATED DEL PEAK 23(17Q21.2) WILD-TYPE 
                            26                             64 
  DEL PEAK 23(17Q21.2) MUTATED DEL PEAK 23(17Q21.2) WILD-TYPE 
                            14                             19 
$`DEL PEAK 23(17Q21.2) MUTATED`
TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC 
       12.59        42.51        13.91        16.11        30.31        57.53 
TCGA-OR-A5JG TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW 
       17.79        49.22        15.25        12.59        66.51        72.39 
TCGA-OR-A5K2 TCGA-OR-A5K9 TCGA-OR-A5KY TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LD 
       32.68        11.31        12.85        28.31         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OU-A5PI 
       21.76        52.24        61.08        79.07        36.03        38.50 
TCGA-P6-A5OH TCGA-PK-A5HA 
        0.00        39.48 

$`DEL PEAK 23(17Q21.2) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-OR-A5J1 TCGA-OR-A5J2 
       33.83        91.30        43.30        39.58        44.55        55.13 
TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB 
       68.75        12.00        88.87        19.04        44.45        18.12 
TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       99.88        69.21        66.25        69.37        76.64        16.11 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       67.59        18.48        39.25        36.26       121.25        29.82 
TCGA-OR-A5JU TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 
        9.50        31.23        18.15        27.02       108.13       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO 
       35.57        16.37        49.08        24.62        24.36        46.49 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       88.01        83.80        95.18       153.63       127.50        68.25 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LI 
       29.10        28.64        23.64        14.63        78.41        14.33 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        90.08        53.03        77.00        61.05        28.04 
TCGA-OR-A5LT TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       18.05        24.85        20.25        22.32 

  DEL PEAK 23(17Q21.2) MUTATED DEL PEAK 23(17Q21.2) WILD-TYPE 
                          0.00                           4.11 
  DEL PEAK 23(17Q21.2) MUTATED DEL PEAK 23(17Q21.2) WILD-TYPE 
                         79.07                         153.63 
  DEL PEAK 23(17Q21.2) MUTATED DEL PEAK 23(17Q21.2) WILD-TYPE 
                        31.495                         43.875 
[1] "0.0 - 79.1 (31.5)"  "4.1 - 153.6 (43.9)"
[1] "hr=" "2.7"
D41V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 23(17Q21.2) MUTATED         1       10         4        9
  DEL PEAK 23(17Q21.2) WILD-TYPE       8       33        14        9
D41V3, multiclass
           clus
vv          DEL PEAK 23(17Q21.2) MUTATED DEL PEAK 23(17Q21.2) WILD-TYPE
  STAGE I                              1                              8
  STAGE II                            10                             33
  STAGE III                            4                             14
  STAGE IV                             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"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 23(17Q21.2) MUTATED    1 11  3  9
  DEL PEAK 23(17Q21.2) WILD-TYPE  8 37  8 11
D41V4, multiclass
    clus
vv   DEL PEAK 23(17Q21.2) MUTATED DEL PEAK 23(17Q21.2) WILD-TYPE
  T1                            1                              8
  T2                           11                             37
  T3                            3                              8
  T4                            9                             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"
D41V5, binary
                                cls
clus                              0  1
  DEL PEAK 23(17Q21.2) MUTATED   20  4
  DEL PEAK 23(17Q21.2) WILD-TYPE 58  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(17Q21.2) MUTATED     20    4
  DEL PEAK 23(17Q21.2) WILD-TYPE   58    6
   clus
vv  DEL PEAK 23(17Q21.2) MUTATED DEL PEAK 23(17Q21.2) WILD-TYPE
  0                           20                             58
  1                            4                              6
[1] 2 2
[1] FALSE
D41V6, binary
                                cls
clus                              0  1
  DEL PEAK 23(17Q21.2) MUTATED   13 13
  DEL PEAK 23(17Q21.2) WILD-TYPE 46 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(17Q21.2) MUTATED     13   13
  DEL PEAK 23(17Q21.2) WILD-TYPE   46   18
        clus
vv       DEL PEAK 23(17Q21.2) MUTATED DEL PEAK 23(17Q21.2) WILD-TYPE
  FEMALE                           13                             46
  MALE                             13                             18
[1] 2 2
[1] FALSE
D41V7, binary
                                cls
clus                              0  1
  DEL PEAK 23(17Q21.2) MUTATED   19  5
  DEL PEAK 23(17Q21.2) WILD-TYPE 50 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(17Q21.2) MUTATED     19    5
  DEL PEAK 23(17Q21.2) WILD-TYPE   50   13
     clus
vv    DEL PEAK 23(17Q21.2) MUTATED DEL PEAK 23(17Q21.2) WILD-TYPE
  NO                            19                             50
  YES                            5                             13
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK 23(17Q21.2) MUTATED                                       0
  DEL PEAK 23(17Q21.2) WILD-TYPE                                     1
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK 23(17Q21.2) MUTATED                                          0
  DEL PEAK 23(17Q21.2) WILD-TYPE                                        4
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK 23(17Q21.2) MUTATED                                     26
  DEL PEAK 23(17Q21.2) WILD-TYPE                                   59
D41V8, multiclass
                                          clus
vv                                         DEL PEAK 23(17Q21.2) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               26
                                          clus
vv                                         DEL PEAK 23(17Q21.2) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 23(17Q21.2) MUTATED   12  3  6  2
  DEL PEAK 23(17Q21.2) WILD-TYPE 51  4  6  3
D41V9, multiclass
    clus
vv   DEL PEAK 23(17Q21.2) MUTATED DEL PEAK 23(17Q21.2) WILD-TYPE
  R0                           12                             51
  R1                            3                              4
  R2                            6                              6
  RX                            2                              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"
D41V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(17Q21.2) MUTATED       0                         0    21
  DEL PEAK 23(17Q21.2) WILD-TYPE     2                         1    55
D41V11, multiclass
                           clus
vv                          DEL PEAK 23(17Q21.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               21
                           clus
vv                          DEL PEAK 23(17Q21.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V12, binary
                                cls
clus                              0  1
  DEL PEAK 23(17Q21.2) MUTATED    2  9
  DEL PEAK 23(17Q21.2) WILD-TYPE  6 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(17Q21.2) MUTATED      2    9
  DEL PEAK 23(17Q21.2) WILD-TYPE    6   29
                        clus
vv                       DEL PEAK 23(17Q21.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                            9
                        clus
vv                       DEL PEAK 23(17Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             29
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 24(17Q24.2) MUTATION ANALYSIS
D42V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 24(17Q24.2) MUTATED   12 12
  DEL PEAK 24(17Q24.2) WILD-TYPE 45 21
  DEL PEAK 24(17Q24.2) MUTATED DEL PEAK 24(17Q24.2) WILD-TYPE 
                            24                             66 
  DEL PEAK 24(17Q24.2) MUTATED DEL PEAK 24(17Q24.2) WILD-TYPE 
                            12                             21 
$`DEL PEAK 24(17Q24.2) MUTATED`
TCGA-OR-A5LB TCGA-P6-A5OG TCGA-PK-A5HB TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5JA 
       39.58        12.59        42.51        13.91        16.11        30.31 
TCGA-OR-A5JC TCGA-OR-A5JG TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JS TCGA-OR-A5JV 
       57.53        17.79        49.22        18.48        12.59        66.51 
TCGA-OR-A5JW TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KY TCGA-OR-A5L6 TCGA-OR-A5LC 
       72.39        49.08        11.31        12.85        28.31         5.23 
TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LM TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA 
       21.76        52.24        61.08        36.03        38.50        39.48 

$`DEL PEAK 24(17Q24.2) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-OR-A5L5 TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 
       33.83        91.30        43.30        44.55        55.13        68.75 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD 
       12.00        88.87        19.04        44.45        18.12        99.88 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL 
       69.21        66.25        69.37        76.64        16.11        67.59 
TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU 
       39.25        15.25        36.26       121.25        29.82         9.50 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       31.23        18.15        27.02       108.13        32.68       113.92 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ 
       35.57        16.37        24.62        24.36        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        68.25        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L8 
        4.11        58.55        60.89       152.15        31.79        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LI 
       28.64        23.64        39.35        14.63        78.41        14.33 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP 
       36.33        90.08        53.03        77.00        79.07        61.05 
TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       28.04        18.05         0.00        24.85        20.25        22.32 

  DEL PEAK 24(17Q24.2) MUTATED DEL PEAK 24(17Q24.2) WILD-TYPE 
                          5.23                           0.00 
  DEL PEAK 24(17Q24.2) MUTATED DEL PEAK 24(17Q24.2) WILD-TYPE 
                         72.39                         153.63 
  DEL PEAK 24(17Q24.2) MUTATED DEL PEAK 24(17Q24.2) WILD-TYPE 
                        33.170                         41.325 
[1] "5.2 - 72.4 (33.2)"  "0.0 - 153.6 (41.3)"
[1] "hr=" "2.3"
D42V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 24(17Q24.2) MUTATED         1        9         2       10
  DEL PEAK 24(17Q24.2) WILD-TYPE       8       34        16        8
D42V3, multiclass
           clus
vv          DEL PEAK 24(17Q24.2) MUTATED DEL PEAK 24(17Q24.2) WILD-TYPE
  STAGE I                              1                              8
  STAGE II                             9                             34
  STAGE III                            2                             16
  STAGE IV                            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"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 24(17Q24.2) MUTATED    1 10  3  8
  DEL PEAK 24(17Q24.2) WILD-TYPE  8 38  8 12
D42V4, multiclass
    clus
vv   DEL PEAK 24(17Q24.2) MUTATED DEL PEAK 24(17Q24.2) WILD-TYPE
  T1                            1                              8
  T2                           10                             38
  T3                            3                              8
  T4                            8                             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"
D42V5, binary
                                cls
clus                              0  1
  DEL PEAK 24(17Q24.2) MUTATED   18  4
  DEL PEAK 24(17Q24.2) WILD-TYPE 60  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(17Q24.2) MUTATED     18    4
  DEL PEAK 24(17Q24.2) WILD-TYPE   60    6
   clus
vv  DEL PEAK 24(17Q24.2) MUTATED DEL PEAK 24(17Q24.2) WILD-TYPE
  0                           18                             60
  1                            4                              6
[1] 2 2
[1] FALSE
D42V6, binary
                                cls
clus                              0  1
  DEL PEAK 24(17Q24.2) MUTATED   12 12
  DEL PEAK 24(17Q24.2) WILD-TYPE 47 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(17Q24.2) MUTATED     12   12
  DEL PEAK 24(17Q24.2) WILD-TYPE   47   19
        clus
vv       DEL PEAK 24(17Q24.2) MUTATED DEL PEAK 24(17Q24.2) WILD-TYPE
  FEMALE                           12                             47
  MALE                             12                             19
[1] 2 2
[1] FALSE
D42V7, binary
                                cls
clus                              0  1
  DEL PEAK 24(17Q24.2) MUTATED   16  6
  DEL PEAK 24(17Q24.2) WILD-TYPE 53 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(17Q24.2) MUTATED     16    6
  DEL PEAK 24(17Q24.2) WILD-TYPE   53   12
     clus
vv    DEL PEAK 24(17Q24.2) MUTATED DEL PEAK 24(17Q24.2) WILD-TYPE
  NO                            16                             53
  YES                            6                             12
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK 24(17Q24.2) MUTATED                                       0
  DEL PEAK 24(17Q24.2) WILD-TYPE                                     1
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK 24(17Q24.2) MUTATED                                          0
  DEL PEAK 24(17Q24.2) WILD-TYPE                                        4
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK 24(17Q24.2) MUTATED                                     24
  DEL PEAK 24(17Q24.2) WILD-TYPE                                   61
D42V8, multiclass
                                          clus
vv                                         DEL PEAK 24(17Q24.2) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               24
                                          clus
vv                                         DEL PEAK 24(17Q24.2) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 24(17Q24.2) MUTATED   11  4  5  1
  DEL PEAK 24(17Q24.2) WILD-TYPE 52  3  7  4
D42V9, multiclass
    clus
vv   DEL PEAK 24(17Q24.2) MUTATED DEL PEAK 24(17Q24.2) WILD-TYPE
  R0                           11                             52
  R1                            4                              3
  R2                            5                              7
  RX                            1                              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"
D42V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(17Q24.2) MUTATED       0                         0    20
  DEL PEAK 24(17Q24.2) WILD-TYPE     2                         1    56
D42V11, multiclass
                           clus
vv                          DEL PEAK 24(17Q24.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               20
                           clus
vv                          DEL PEAK 24(17Q24.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V12, binary
                                cls
clus                              0  1
  DEL PEAK 24(17Q24.2) MUTATED    2  9
  DEL PEAK 24(17Q24.2) WILD-TYPE  6 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(17Q24.2) MUTATED      2    9
  DEL PEAK 24(17Q24.2) WILD-TYPE    6   29
                        clus
vv                       DEL PEAK 24(17Q24.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                            9
                        clus
vv                       DEL PEAK 24(17Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             29
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 25(20P12.1) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 25(20P12.1) MUTATED    6  6
  DEL PEAK 25(20P12.1) WILD-TYPE 51 27
  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                            12                             78 
  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                             6                             27 
$`DEL PEAK 25(20P12.1) MUTATED`
TCGA-OR-A5K0 TCGA-OR-A5KP TCGA-PK-A5HB TCGA-OR-A5J2 TCGA-OR-A5J7 TCGA-OR-A5JA 
       33.83        91.30        42.51        55.13        16.11        30.31 
TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5JS TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-PK-A5HC 
       18.12        18.48        12.59        11.31        24.36        22.32 

$`DEL PEAK 25(20P12.1) WILD-TYPE`
TCGA-OR-A5L5 TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 
       43.30        39.58        12.59        44.55        68.75        13.91 
TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JD 
       12.00        88.87        19.04        44.45        57.53        99.88 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        66.25        17.79        69.37        76.64        16.11 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       49.22        67.59        39.25        15.25        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       29.82         9.50        66.51        72.39        31.23        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       27.02       108.13        32.68       113.92        35.57        16.37 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       49.08        24.62        46.49        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       127.50        68.25        44.84        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5L8 
       58.55        60.89       152.15        31.79        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       28.64        23.64         5.23        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       52.24        78.41        14.33        36.33        90.08        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        77.00        79.07        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       18.05        38.50         0.00        24.85        20.25        39.48 

  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                         11.31                           0.00 
  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                         91.30                         153.63 
  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE 
                         23.34                          39.53 
[1] "11.3 - 91.3 (23.3)" "0.0 - 153.6 (39.5)"
[1] "hr=" "2"  
D43V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 25(20P12.1) MUTATED         0        5         2        4
  DEL PEAK 25(20P12.1) WILD-TYPE       9       38        16       14
D43V3, multiclass
           clus
vv          DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE
  STAGE I                              0                              9
  STAGE II                             5                             38
  STAGE III                            2                             16
  STAGE IV                             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"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 25(20P12.1) MUTATED    0  5  2  4
  DEL PEAK 25(20P12.1) WILD-TYPE  9 43  9 16
D43V4, multiclass
    clus
vv   DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE
  T1                            0                              9
  T2                            5                             43
  T3                            2                              9
  T4                            4                             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"
D43V5, binary
                                cls
clus                              0  1
  DEL PEAK 25(20P12.1) MUTATED   11  0
  DEL PEAK 25(20P12.1) WILD-TYPE 67 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(20P12.1) MUTATED     11    0
  DEL PEAK 25(20P12.1) WILD-TYPE   67   10
   clus
vv  DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE
  0                           11                             67
  1                            0                             10
[1] 2 2
[1] FALSE
D43V6, binary
                                cls
clus                              0  1
  DEL PEAK 25(20P12.1) MUTATED   10  2
  DEL PEAK 25(20P12.1) WILD-TYPE 49 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(20P12.1) MUTATED     10    2
  DEL PEAK 25(20P12.1) WILD-TYPE   49   29
        clus
vv       DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE
  FEMALE                           10                             49
  MALE                              2                             29
[1] 2 2
[1] FALSE
D43V7, binary
                                cls
clus                              0  1
  DEL PEAK 25(20P12.1) MUTATED    8  3
  DEL PEAK 25(20P12.1) WILD-TYPE 61 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(20P12.1) MUTATED      8    3
  DEL PEAK 25(20P12.1) WILD-TYPE   61   15
     clus
vv    DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE
  NO                             8                             61
  YES                            3                             15
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK 25(20P12.1) MUTATED                                       0
  DEL PEAK 25(20P12.1) WILD-TYPE                                     1
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK 25(20P12.1) MUTATED                                          0
  DEL PEAK 25(20P12.1) WILD-TYPE                                        4
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK 25(20P12.1) MUTATED                                     12
  DEL PEAK 25(20P12.1) WILD-TYPE                                   73
D43V8, multiclass
                                          clus
vv                                         DEL PEAK 25(20P12.1) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            0
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               12
                                          clus
vv                                         DEL PEAK 25(20P12.1) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              4
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 25(20P12.1) MUTATED    5  5  1  0
  DEL PEAK 25(20P12.1) WILD-TYPE 58  2 11  5
D43V9, multiclass
    clus
vv   DEL PEAK 25(20P12.1) MUTATED DEL PEAK 25(20P12.1) WILD-TYPE
  R0                            5                             58
  R1                            5                              2
  R2                            1                             11
  RX                            0                              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"
D43V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(20P12.1) MUTATED       1                         0    10
  DEL PEAK 25(20P12.1) WILD-TYPE     1                         1    66
D43V11, multiclass
                           clus
vv                          DEL PEAK 25(20P12.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               10
                           clus
vv                          DEL PEAK 25(20P12.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V12, binary
                                cls
clus                              0  1
  DEL PEAK 25(20P12.1) MUTATED    2  3
  DEL PEAK 25(20P12.1) WILD-TYPE  6 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(20P12.1) MUTATED      2    3
  DEL PEAK 25(20P12.1) WILD-TYPE    6   35
                        clus
vv                       DEL PEAK 25(20P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                            3
                        clus
vv                       DEL PEAK 25(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                             35
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 26(22Q12.1) MUTATION ANALYSIS
D44V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 26(22Q12.1) MUTATED   27 23
  DEL PEAK 26(22Q12.1) WILD-TYPE 30 10
  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE 
                            50                             40 
  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE 
                            23                             10 
$`DEL PEAK 26(22Q12.1) MUTATED`
TCGA-OR-A5KP TCGA-OR-A5LB TCGA-P6-A5OG TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J6 
       91.30        39.58        12.59        55.13        68.75        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
       16.11        19.04        44.45        30.31        18.12        57.53 
TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       99.88        69.21        17.79        69.37        76.64        49.22 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW 
       15.25        36.26       121.25         9.50        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO 
       31.23        18.15        32.68        16.37        11.31        46.49 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L6 
       88.01        83.80        44.84        12.85         4.11        28.31 
TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LM 
        5.23        21.76        52.24        14.33        53.03        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OH 
       77.00        79.07        36.03        18.05        38.50         0.00 
TCGA-PK-A5H9 TCGA-PK-A5HA 
       20.25        39.48 

$`DEL PEAK 26(22Q12.1) WILD-TYPE`
TCGA-OR-A5K0 TCGA-OR-A5L5 TCGA-PK-A5HB TCGA-OR-A5J1 TCGA-OR-A5J4 TCGA-OR-A5J5 
       33.83        43.30        42.51        44.55        13.91        12.00 
TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JS 
       66.25        16.11        67.59        18.48        39.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 
       29.82        27.02       108.13       113.92        35.57        49.08 
TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       24.62        24.36        95.18       153.63       127.50        68.25 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5L9 
       58.55        60.89       152.15        31.79        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       23.64        39.35        14.63        78.41        36.33        90.08 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG TCGA-PK-A5HC 
       61.05        28.04        24.85        22.32 

  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE 
                             0                             12 
  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 
                         38.99                          37.79 
[1] "0.0 - 121.2 (39.0)"  "12.0 - 153.6 (37.8)"
[1] "hr=" "2"  
D44V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 26(22Q12.1) MUTATED         4       21        10       14
  DEL PEAK 26(22Q12.1) WILD-TYPE       5       22         8        4
D44V3, multiclass
           clus
vv          DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE
  STAGE I                              4                              5
  STAGE II                            21                             22
  STAGE III                           10                              8
  STAGE IV                            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"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 26(22Q12.1) MUTATED    4 23  9 13
  DEL PEAK 26(22Q12.1) WILD-TYPE  5 25  2  7
D44V4, multiclass
    clus
vv   DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE
  T1                            4                              5
  T2                           23                             25
  T3                            9                              2
  T4                           13                              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"
D44V5, binary
                                cls
clus                              0  1
  DEL PEAK 26(22Q12.1) MUTATED   44  5
  DEL PEAK 26(22Q12.1) WILD-TYPE 34  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(22Q12.1) MUTATED     44    5
  DEL PEAK 26(22Q12.1) WILD-TYPE   34    5
   clus
vv  DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE
  0                           44                             34
  1                            5                              5
[1] 2 2
[1] FALSE
D44V6, binary
                                cls
clus                              0  1
  DEL PEAK 26(22Q12.1) MUTATED   30 20
  DEL PEAK 26(22Q12.1) WILD-TYPE 29 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(22Q12.1) MUTATED     30   20
  DEL PEAK 26(22Q12.1) WILD-TYPE   29   11
        clus
vv       DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE
  FEMALE                           30                             29
  MALE                             20                             11
[1] 2 2
[1] FALSE
D44V7, binary
                                cls
clus                              0  1
  DEL PEAK 26(22Q12.1) MUTATED   38  9
  DEL PEAK 26(22Q12.1) WILD-TYPE 31  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(22Q12.1) MUTATED     38    9
  DEL PEAK 26(22Q12.1) WILD-TYPE   31    9
     clus
vv    DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE
  NO                            38                             31
  YES                            9                              9
[1] 2 2
[1] FALSE
                                vv
clus                             ADRENOCORTICAL CARCINOMA- MYXOID TYPE
  DEL PEAK 26(22Q12.1) MUTATED                                       1
  DEL PEAK 26(22Q12.1) WILD-TYPE                                     0
                                vv
clus                             ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE
  DEL PEAK 26(22Q12.1) MUTATED                                          2
  DEL PEAK 26(22Q12.1) WILD-TYPE                                        2
                                vv
clus                             ADRENOCORTICAL CARCINOMA- USUAL TYPE
  DEL PEAK 26(22Q12.1) MUTATED                                     47
  DEL PEAK 26(22Q12.1) WILD-TYPE                                   38
D44V8, multiclass
                                          clus
vv                                         DEL PEAK 26(22Q12.1) MUTATED
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                               1
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                            2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                               47
                                          clus
vv                                         DEL PEAK 26(22Q12.1) WILD-TYPE
  ADRENOCORTICAL CARCINOMA- MYXOID TYPE                                 0
  ADRENOCORTICAL CARCINOMA- ONCOCYTIC TYPE                              2
  ADRENOCORTICAL CARCINOMA- USUAL TYPE                                 38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 26(22Q12.1) MUTATED   34  4  8  2
  DEL PEAK 26(22Q12.1) WILD-TYPE 29  3  4  3
D44V9, multiclass
    clus
vv   DEL PEAK 26(22Q12.1) MUTATED DEL PEAK 26(22Q12.1) WILD-TYPE
  R0                           34                             29
  R1                            4                              3
  R2                            8                              4
  RX                            2                              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"
D44V10, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(22Q12.1) MUTATED       1                         1    41
  DEL PEAK 26(22Q12.1) WILD-TYPE     1                         0    35
D44V11, multiclass
                           clus
vv                          DEL PEAK 26(22Q12.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               41
                           clus
vv                          DEL PEAK 26(22Q12.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                 35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V12, binary
                                cls
clus                              0  1
  DEL PEAK 26(22Q12.1) MUTATED    6 17
  DEL PEAK 26(22Q12.1) WILD-TYPE  2 21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(22Q12.1) MUTATED      6   17
  DEL PEAK 26(22Q12.1) WILD-TYPE    2   21
                        clus
vv                       DEL PEAK 26(22Q12.1) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           17
                        clus
vv                       DEL PEAK 26(22Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             21
[1] 2 2
[1] FALSE
